diff --git a/CHANGELOG.md b/CHANGELOG.md
index ea27be51..c7e9d666 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -5,6 +5,17 @@ All notable changes to the beads project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [Unreleased]
+
+### Added
+
+- **External hook manager detection** - `bd doctor` now detects lefthook, husky, pre-commit, and other hook managers
+  - Checks if external managers have `bd hooks run` integration configured
+  - Reports which hooks have bd integration vs which are missing
+  - `bd doctor --fix` uses `--chain` flag when external managers detected to preserve existing hooks
+  - Supports YAML, TOML, and JSON config formats for lefthook
+  - Detects active manager from git hooks when multiple managers present
+
 ## [0.44.0] - 2026-01-04
 
 ### Added
diff --git a/cmd/bd/doctor/fix/hooks.go b/cmd/bd/doctor/fix/hooks.go
index d46131b1..789ee0cf 100644
--- a/cmd/bd/doctor/fix/hooks.go
+++ b/cmd/bd/doctor/fix/hooks.go
@@ -1,12 +1,354 @@
 package fix
 
 import (
+	"encoding/json"
 	"fmt"
 	"os"
 	"os/exec"
+	"path/filepath"
+	"regexp"
+	"strings"
+
+	"github.com/BurntSushi/toml"
+	"gopkg.in/yaml.v3"
 )
 
-// GitHooks fixes missing or broken git hooks by calling bd hooks install
+// ExternalHookManager represents a detected external hook management tool.
+type ExternalHookManager struct {
+	Name       string // e.g., "lefthook", "husky", "pre-commit"
+	ConfigFile string // Path to the config file that was detected
+}
+
+// hookManagerConfig pairs a manager name with its possible config files.
+type hookManagerConfig struct {
+	name        string
+	configFiles []string
+}
+
+// hookManagerConfigs defines external hook managers in priority order.
+// See https://lefthook.dev/configuration/ for lefthook config options.
+var hookManagerConfigs = []hookManagerConfig{
+	{"lefthook", []string{
+		// YAML variants
+		"lefthook.yml", ".lefthook.yml", ".config/lefthook.yml",
+		"lefthook.yaml", ".lefthook.yaml", ".config/lefthook.yaml",
+		// TOML variants
+		"lefthook.toml", ".lefthook.toml", ".config/lefthook.toml",
+		// JSON variants
+		"lefthook.json", ".lefthook.json", ".config/lefthook.json",
+	}},
+	{"husky", []string{".husky"}},
+	{"pre-commit", []string{".pre-commit-config.yaml", ".pre-commit-config.yml"}},
+	{"overcommit", []string{".overcommit.yml"}},
+	{"yorkie", []string{".yorkie"}},
+	{"simple-git-hooks", []string{
+		".simple-git-hooks.cjs", ".simple-git-hooks.js",
+		"simple-git-hooks.cjs", "simple-git-hooks.js",
+	}},
+}
+
+// DetectExternalHookManagers checks for presence of external hook management tools.
+// Returns a list of detected managers along with their config file paths.
+func DetectExternalHookManagers(path string) []ExternalHookManager {
+	var managers []ExternalHookManager
+
+	for _, mgr := range hookManagerConfigs {
+		for _, configFile := range mgr.configFiles {
+			configPath := filepath.Join(path, configFile)
+			if info, err := os.Stat(configPath); err == nil {
+				// For directories like .husky, check if it exists
+				// For files, check if it's a regular file
+				if info.IsDir() || info.Mode().IsRegular() {
+					managers = append(managers, ExternalHookManager{
+						Name:       mgr.name,
+						ConfigFile: configFile,
+					})
+					break // Only report each manager once
+				}
+			}
+		}
+	}
+
+	return managers
+}
+
+// HookIntegrationStatus represents the status of bd integration in an external hook manager.
+type HookIntegrationStatus struct {
+	Manager          string   // Hook manager name
+	HooksWithBd      []string // Hooks that have bd integration (bd hooks run)
+	HooksWithoutBd   []string // Hooks configured but without bd integration
+	HooksNotInConfig []string // Recommended hooks not in config at all
+	Configured       bool     // Whether any bd integration was found
+}
+
+// bdHookPattern matches the recommended bd hooks run pattern with word boundaries
+var bdHookPattern = regexp.MustCompile(`\bbd\s+hooks\s+run\b`)
+
+// hookManagerPattern pairs a manager name with its detection pattern.
+type hookManagerPattern struct {
+	name    string
+	pattern *regexp.Regexp
+}
+
+// hookManagerPatterns identifies which hook manager installed a git hook (in priority order).
+var hookManagerPatterns = []hookManagerPattern{
+	{"lefthook", regexp.MustCompile(`(?i)lefthook`)},
+	{"husky", regexp.MustCompile(`(?i)(\.husky|husky\.sh)`)},
+	{"pre-commit", regexp.MustCompile(`(?i)(pre-commit\s+run|\.pre-commit-config|INSTALL_PYTHON|PRE_COMMIT)`)},
+	{"simple-git-hooks", regexp.MustCompile(`(?i)simple-git-hooks`)},
+}
+
+// DetectActiveHookManager reads the git hooks to determine which manager installed them.
+// This is more reliable than just checking for config files when multiple managers exist.
+func DetectActiveHookManager(path string) string {
+	// Get git dir
+	cmd := exec.Command("git", "rev-parse", "--git-dir")
+	cmd.Dir = path
+	output, err := cmd.Output()
+	if err != nil {
+		return ""
+	}
+	gitDir := strings.TrimSpace(string(output))
+	if !filepath.IsAbs(gitDir) {
+		gitDir = filepath.Join(path, gitDir)
+	}
+
+	// Check for custom hooks path (core.hooksPath)
+	hooksDir := filepath.Join(gitDir, "hooks")
+	hooksPathCmd := exec.Command("git", "config", "--get", "core.hooksPath")
+	hooksPathCmd.Dir = path
+	if hooksPathOutput, err := hooksPathCmd.Output(); err == nil {
+		customPath := strings.TrimSpace(string(hooksPathOutput))
+		if customPath != "" {
+			if !filepath.IsAbs(customPath) {
+				customPath = filepath.Join(path, customPath)
+			}
+			hooksDir = customPath
+		}
+	}
+
+	// Check common hooks for manager signatures
+	for _, hookName := range []string{"pre-commit", "pre-push", "post-merge"} {
+		hookPath := filepath.Join(hooksDir, hookName)
+		content, err := os.ReadFile(hookPath) // #nosec G304 - path is validated
+		if err != nil {
+			continue
+		}
+		contentStr := string(content)
+
+		// Check each manager pattern (deterministic order)
+		for _, mp := range hookManagerPatterns {
+			if mp.pattern.MatchString(contentStr) {
+				return mp.name
+			}
+		}
+	}
+
+	return ""
+}
+
+// recommendedBdHooks are the hooks that should have bd integration
+var recommendedBdHooks = []string{"pre-commit", "post-merge", "pre-push"}
+
+// lefthookConfigFiles lists lefthook config files (derived from hookManagerConfigs).
+// Format is inferred from extension.
+var lefthookConfigFiles = hookManagerConfigs[0].configFiles // lefthook is first
+
+// CheckLefthookBdIntegration parses lefthook config (YAML, TOML, or JSON) and checks if bd hooks are integrated.
+// See https://lefthook.dev/configuration/ for supported config file locations.
+func CheckLefthookBdIntegration(path string) *HookIntegrationStatus {
+	// Find first existing config file
+	var configPath string
+	for _, name := range lefthookConfigFiles {
+		p := filepath.Join(path, name)
+		if _, err := os.Stat(p); err == nil {
+			configPath = p
+			break
+		}
+	}
+	if configPath == "" {
+		return nil
+	}
+
+	content, err := os.ReadFile(configPath) // #nosec G304 - path is validated
+	if err != nil {
+		return nil
+	}
+
+	// Parse config based on extension
+	var config map[string]interface{}
+	ext := filepath.Ext(configPath)
+	switch ext {
+	case ".toml":
+		if _, err := toml.Decode(string(content), &config); err != nil {
+			return nil
+		}
+	case ".json":
+		if err := json.Unmarshal(content, &config); err != nil {
+			return nil
+		}
+	default: // .yml, .yaml
+		if err := yaml.Unmarshal(content, &config); err != nil {
+			return nil
+		}
+	}
+
+	status := &HookIntegrationStatus{
+		Manager:    "lefthook",
+		Configured: false,
+	}
+
+	// Check each recommended hook
+	for _, hookName := range recommendedBdHooks {
+		hookSection, ok := config[hookName]
+		if !ok {
+			// Hook not configured at all in lefthook
+			status.HooksNotInConfig = append(status.HooksNotInConfig, hookName)
+			continue
+		}
+
+		// Walk to commands.*.run to check for bd hooks run
+		if hasBdInCommands(hookSection) {
+			status.HooksWithBd = append(status.HooksWithBd, hookName)
+			status.Configured = true
+		} else {
+			// Hook is in config but has no bd integration
+			status.HooksWithoutBd = append(status.HooksWithoutBd, hookName)
+		}
+	}
+
+	return status
+}
+
+// hasBdInCommands checks if any command's "run" field contains bd hooks run.
+// Walks the lefthook structure: hookSection.commands.*.run
+func hasBdInCommands(hookSection interface{}) bool {
+	sectionMap, ok := hookSection.(map[string]interface{})
+	if !ok {
+		return false
+	}
+
+	commands, ok := sectionMap["commands"]
+	if !ok {
+		return false
+	}
+
+	commandsMap, ok := commands.(map[string]interface{})
+	if !ok {
+		return false
+	}
+
+	for _, cmdConfig := range commandsMap {
+		cmdMap, ok := cmdConfig.(map[string]interface{})
+		if !ok {
+			continue
+		}
+
+		runVal, ok := cmdMap["run"]
+		if !ok {
+			continue
+		}
+
+		runStr, ok := runVal.(string)
+		if !ok {
+			continue
+		}
+
+		if bdHookPattern.MatchString(runStr) {
+			return true
+		}
+	}
+
+	return false
+}
+
+// CheckHuskyBdIntegration checks .husky/ scripts for bd integration.
+func CheckHuskyBdIntegration(path string) *HookIntegrationStatus {
+	huskyDir := filepath.Join(path, ".husky")
+	if _, err := os.Stat(huskyDir); os.IsNotExist(err) {
+		return nil
+	}
+
+	status := &HookIntegrationStatus{
+		Manager:    "husky",
+		Configured: false,
+	}
+
+	for _, hookName := range recommendedBdHooks {
+		hookPath := filepath.Join(huskyDir, hookName)
+		content, err := os.ReadFile(hookPath) // #nosec G304 - path is validated
+		if err != nil {
+			// Hook script doesn't exist in .husky/
+			status.HooksNotInConfig = append(status.HooksNotInConfig, hookName)
+			continue
+		}
+
+		contentStr := string(content)
+
+		// Check for bd hooks run pattern
+		if bdHookPattern.MatchString(contentStr) {
+			status.HooksWithBd = append(status.HooksWithBd, hookName)
+			status.Configured = true
+		} else {
+			status.HooksWithoutBd = append(status.HooksWithoutBd, hookName)
+		}
+	}
+
+	return status
+}
+
+// checkManagerBdIntegration checks a specific manager for bd integration.
+func checkManagerBdIntegration(name, path string) *HookIntegrationStatus {
+	switch name {
+	case "lefthook":
+		return CheckLefthookBdIntegration(path)
+	case "husky":
+		return CheckHuskyBdIntegration(path)
+	default:
+		return nil
+	}
+}
+
+// CheckExternalHookManagerIntegration checks if detected hook managers have bd integration.
+func CheckExternalHookManagerIntegration(path string) *HookIntegrationStatus {
+	managers := DetectExternalHookManagers(path)
+	if len(managers) == 0 {
+		return nil
+	}
+
+	// First, try to detect which manager is actually active from git hooks
+	if activeManager := DetectActiveHookManager(path); activeManager != "" {
+		if status := checkManagerBdIntegration(activeManager, path); status != nil {
+			return status
+		}
+	}
+
+	// Fall back to checking detected managers in order
+	for _, m := range managers {
+		if status := checkManagerBdIntegration(m.Name, path); status != nil {
+			return status
+		}
+	}
+
+	// Return basic status for unsupported managers
+	return &HookIntegrationStatus{
+		Manager:    ManagerNames(managers),
+		Configured: false,
+	}
+}
+
+// ManagerNames extracts names from a slice of ExternalHookManager as comma-separated string.
+func ManagerNames(managers []ExternalHookManager) string {
+	names := make([]string, len(managers))
+	for i, m := range managers {
+		names[i] = m.Name
+	}
+	return strings.Join(names, ", ")
+}
+
+// GitHooks fixes missing or broken git hooks by calling bd hooks install.
+// If external hook managers are detected (lefthook, husky, etc.), it uses
+// --chain to preserve existing hooks instead of overwriting them.
 func GitHooks(path string) error {
 	// Validate workspace
 	if err := validateBeadsWorkspace(path); err != nil {
@@ -21,15 +363,26 @@ func GitHooks(path string) error {
 		return fmt.Errorf("not a git repository")
 	}
 
+	// Detect external hook managers
+	externalManagers := DetectExternalHookManagers(path)
+
 	// Get bd binary path
 	bdBinary, err := getBdBinary()
 	if err != nil {
 		return err
 	}
 
+	// Build command arguments
+	args := []string{"hooks", "install"}
+
+	// If external hook managers detected, use --chain to preserve them
+	if len(externalManagers) > 0 {
+		args = append(args, "--chain")
+	}
+
 	// Run bd hooks install
-	cmd := newBdCmd(bdBinary, "hooks", "install")
-	cmd.Dir = path                                     // Set working directory without changing process dir
+	cmd := newBdCmd(bdBinary, args...)
+	cmd.Dir = path // Set working directory without changing process dir
 	cmd.Stdout = os.Stdout
 	cmd.Stderr = os.Stderr
 
diff --git a/cmd/bd/doctor/fix/hooks_test.go b/cmd/bd/doctor/fix/hooks_test.go
new file mode 100644
index 00000000..9e92de70
--- /dev/null
+++ b/cmd/bd/doctor/fix/hooks_test.go
@@ -0,0 +1,894 @@
+package fix
+
+import (
+	"os"
+	"os/exec"
+	"path/filepath"
+	"testing"
+)
+
+func TestDetectExternalHookManagers(t *testing.T) {
+	tests := []struct {
+		name     string
+		setup    func(dir string) error
+		expected []string // Expected manager names
+	}{
+		{
+			name: "no hook managers",
+			setup: func(dir string) error {
+				return nil
+			},
+			expected: nil,
+		},
+		{
+			name: "lefthook.yml",
+			setup: func(dir string) error {
+				return os.WriteFile(filepath.Join(dir, "lefthook.yml"), []byte("pre-commit:\n"), 0644)
+			},
+			expected: []string{"lefthook"},
+		},
+		{
+			name: "lefthook.yaml",
+			setup: func(dir string) error {
+				return os.WriteFile(filepath.Join(dir, "lefthook.yaml"), []byte("pre-commit:\n"), 0644)
+			},
+			expected: []string{"lefthook"},
+		},
+		{
+			name: "lefthook.toml",
+			setup: func(dir string) error {
+				return os.WriteFile(filepath.Join(dir, "lefthook.toml"), []byte("[pre-commit]\n"), 0644)
+			},
+			expected: []string{"lefthook"},
+		},
+		{
+			name: "lefthook.json",
+			setup: func(dir string) error {
+				return os.WriteFile(filepath.Join(dir, "lefthook.json"), []byte(`{"pre-commit":{}}`), 0644)
+			},
+			expected: []string{"lefthook"},
+		},
+		{
+			name: ".lefthook.yml (hidden)",
+			setup: func(dir string) error {
+				return os.WriteFile(filepath.Join(dir, ".lefthook.yml"), []byte("pre-commit:\n"), 0644)
+			},
+			expected: []string{"lefthook"},
+		},
+		{
+			name: ".config/lefthook.yml",
+			setup: func(dir string) error {
+				configDir := filepath.Join(dir, ".config")
+				if err := os.MkdirAll(configDir, 0755); err != nil {
+					return err
+				}
+				return os.WriteFile(filepath.Join(configDir, "lefthook.yml"), []byte("pre-commit:\n"), 0644)
+			},
+			expected: []string{"lefthook"},
+		},
+		{
+			name: ".husky directory",
+			setup: func(dir string) error {
+				return os.MkdirAll(filepath.Join(dir, ".husky"), 0755)
+			},
+			expected: []string{"husky"},
+		},
+		{
+			name: ".pre-commit-config.yaml",
+			setup: func(dir string) error {
+				return os.WriteFile(filepath.Join(dir, ".pre-commit-config.yaml"), []byte("repos:\n"), 0644)
+			},
+			expected: []string{"pre-commit"},
+		},
+		{
+			name: ".overcommit.yml",
+			setup: func(dir string) error {
+				return os.WriteFile(filepath.Join(dir, ".overcommit.yml"), []byte("PreCommit:\n"), 0644)
+			},
+			expected: []string{"overcommit"},
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			dir := t.TempDir()
+			if err := tt.setup(dir); err != nil {
+				t.Fatalf("setup failed: %v", err)
+			}
+
+			managers := DetectExternalHookManagers(dir)
+
+			if len(tt.expected) == 0 {
+				if len(managers) != 0 {
+					t.Errorf("expected no managers, got %v", managers)
+				}
+				return
+			}
+
+			if len(managers) != len(tt.expected) {
+				t.Errorf("expected %d managers, got %d", len(tt.expected), len(managers))
+				return
+			}
+
+			for i, exp := range tt.expected {
+				if managers[i].Name != exp {
+					t.Errorf("expected manager %q, got %q", exp, managers[i].Name)
+				}
+			}
+		})
+	}
+}
+
+func TestCheckLefthookBdIntegration(t *testing.T) {
+	tests := []struct {
+		name                 string
+		configFile           string
+		configContent        string
+		expectConfigured     bool
+		expectHooksWithBd    []string
+		expectHooksWithoutBd []string
+		expectNotInConfig    []string
+	}{
+		{
+			name:       "no config",
+			configFile: "",
+			// No file created
+			expectConfigured: false,
+		},
+		{
+			name:       "yaml with bd hooks run",
+			configFile: "lefthook.yml",
+			configContent: `
+pre-commit:
+  commands:
+    bd:
+      run: bd hooks run pre-commit
+post-merge:
+  commands:
+    bd:
+      run: bd hooks run post-merge
+pre-push:
+  commands:
+    bd:
+      run: bd hooks run pre-push
+`,
+			expectConfigured:  true,
+			expectHooksWithBd: []string{"pre-commit", "post-merge", "pre-push"},
+		},
+		{
+			name:       "yaml with partial bd integration",
+			configFile: "lefthook.yml",
+			configContent: `
+pre-commit:
+  commands:
+    bd:
+      run: bd hooks run pre-commit
+    lint:
+      run: eslint .
+post-merge:
+  commands:
+    bd:
+      run: echo "no bd here"
+`,
+			expectConfigured:     true,
+			expectHooksWithBd:    []string{"pre-commit"},
+			expectHooksWithoutBd: []string{"post-merge"},
+			expectNotInConfig:    []string{"pre-push"},
+		},
+		{
+			name:       "yaml without bd at all",
+			configFile: "lefthook.yml",
+			configContent: `
+pre-commit:
+  commands:
+    lint:
+      run: eslint .
+`,
+			expectConfigured:     false,
+			expectHooksWithoutBd: []string{"pre-commit"},
+			expectNotInConfig:    []string{"post-merge", "pre-push"},
+		},
+		{
+			name:       "toml with bd hooks run",
+			configFile: "lefthook.toml",
+			configContent: `
+[pre-commit.commands.bd]
+run = "bd hooks run pre-commit"
+
+[post-merge.commands.bd]
+run = "bd hooks run post-merge"
+
+[pre-push.commands.bd]
+run = "bd hooks run pre-push"
+`,
+			expectConfigured:  true,
+			expectHooksWithBd: []string{"pre-commit", "post-merge", "pre-push"},
+		},
+		{
+			name:       "json with bd hooks run",
+			configFile: "lefthook.json",
+			configContent: `{
+  "pre-commit": {
+    "commands": {
+      "bd": {
+        "run": "bd hooks run pre-commit"
+      }
+    }
+  },
+  "post-merge": {
+    "commands": {
+      "bd": {
+        "run": "bd hooks run post-merge"
+      }
+    }
+  },
+  "pre-push": {
+    "commands": {
+      "bd": {
+        "run": "bd hooks run pre-push"
+      }
+    }
+  }
+}`,
+			expectConfigured:  true,
+			expectHooksWithBd: []string{"pre-commit", "post-merge", "pre-push"},
+		},
+		{
+			name:       "hidden config .lefthook.yml",
+			configFile: ".lefthook.yml",
+			configContent: `
+pre-commit:
+  commands:
+    bd:
+      run: bd hooks run pre-commit
+`,
+			expectConfigured:  true,
+			expectHooksWithBd: []string{"pre-commit"},
+			expectNotInConfig: []string{"post-merge", "pre-push"},
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			dir := t.TempDir()
+
+			if tt.configFile != "" {
+				configPath := filepath.Join(dir, tt.configFile)
+				// Handle .config/ subdirectory
+				if err := os.MkdirAll(filepath.Dir(configPath), 0755); err != nil {
+					t.Fatalf("failed to create config dir: %v", err)
+				}
+				if err := os.WriteFile(configPath, []byte(tt.configContent), 0644); err != nil {
+					t.Fatalf("failed to write config: %v", err)
+				}
+			}
+
+			status := CheckLefthookBdIntegration(dir)
+
+			if tt.configFile == "" {
+				if status != nil {
+					t.Errorf("expected nil status for no config, got %+v", status)
+				}
+				return
+			}
+
+			if status == nil {
+				t.Fatal("expected non-nil status")
+			}
+
+			if status.Configured != tt.expectConfigured {
+				t.Errorf("Configured: expected %v, got %v", tt.expectConfigured, status.Configured)
+			}
+
+			if !slicesEqual(status.HooksWithBd, tt.expectHooksWithBd) {
+				t.Errorf("HooksWithBd: expected %v, got %v", tt.expectHooksWithBd, status.HooksWithBd)
+			}
+
+			if !slicesEqual(status.HooksWithoutBd, tt.expectHooksWithoutBd) {
+				t.Errorf("HooksWithoutBd: expected %v, got %v", tt.expectHooksWithoutBd, status.HooksWithoutBd)
+			}
+
+			if !slicesEqual(status.HooksNotInConfig, tt.expectNotInConfig) {
+				t.Errorf("HooksNotInConfig: expected %v, got %v", tt.expectNotInConfig, status.HooksNotInConfig)
+			}
+		})
+	}
+}
+
+func TestCheckHuskyBdIntegration(t *testing.T) {
+	tests := []struct {
+		name                 string
+		hooks                map[string]string // hookName -> content
+		expectConfigured     bool
+		expectHooksWithBd    []string
+		expectHooksWithoutBd []string
+		expectNotInConfig    []string
+	}{
+		{
+			name:             "no .husky directory",
+			hooks:            nil,
+			expectConfigured: false,
+		},
+		{
+			name: "all hooks with bd",
+			hooks: map[string]string{
+				"pre-commit": "#!/bin/sh\nbd hooks run pre-commit\n",
+				"post-merge": "#!/bin/sh\nbd hooks run post-merge\n",
+				"pre-push":   "#!/bin/sh\nbd hooks run pre-push\n",
+			},
+			expectConfigured:  true,
+			expectHooksWithBd: []string{"pre-commit", "post-merge", "pre-push"},
+		},
+		{
+			name: "partial bd integration",
+			hooks: map[string]string{
+				"pre-commit": "#!/bin/sh\nbd hooks run pre-commit\n",
+				"post-merge": "#!/bin/sh\necho 'no bd'\n",
+			},
+			expectConfigured:     true,
+			expectHooksWithBd:    []string{"pre-commit"},
+			expectHooksWithoutBd: []string{"post-merge"},
+			expectNotInConfig:    []string{"pre-push"},
+		},
+		{
+			name: "no bd at all",
+			hooks: map[string]string{
+				"pre-commit": "#!/bin/sh\neslint .\n",
+			},
+			expectConfigured:     false,
+			expectHooksWithoutBd: []string{"pre-commit"},
+			expectNotInConfig:    []string{"post-merge", "pre-push"},
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			dir := t.TempDir()
+
+			if tt.hooks != nil {
+				huskyDir := filepath.Join(dir, ".husky")
+				if err := os.MkdirAll(huskyDir, 0755); err != nil {
+					t.Fatalf("failed to create .husky: %v", err)
+				}
+				for hookName, content := range tt.hooks {
+					if err := os.WriteFile(filepath.Join(huskyDir, hookName), []byte(content), 0755); err != nil {
+						t.Fatalf("failed to write hook %s: %v", hookName, err)
+					}
+				}
+			}
+
+			status := CheckHuskyBdIntegration(dir)
+
+			if tt.hooks == nil {
+				if status != nil {
+					t.Errorf("expected nil status for no .husky, got %+v", status)
+				}
+				return
+			}
+
+			if status == nil {
+				t.Fatal("expected non-nil status")
+			}
+
+			if status.Configured != tt.expectConfigured {
+				t.Errorf("Configured: expected %v, got %v", tt.expectConfigured, status.Configured)
+			}
+
+			if !slicesEqual(status.HooksWithBd, tt.expectHooksWithBd) {
+				t.Errorf("HooksWithBd: expected %v, got %v", tt.expectHooksWithBd, status.HooksWithBd)
+			}
+
+			if !slicesEqual(status.HooksWithoutBd, tt.expectHooksWithoutBd) {
+				t.Errorf("HooksWithoutBd: expected %v, got %v", tt.expectHooksWithoutBd, status.HooksWithoutBd)
+			}
+
+			if !slicesEqual(status.HooksNotInConfig, tt.expectNotInConfig) {
+				t.Errorf("HooksNotInConfig: expected %v, got %v", tt.expectNotInConfig, status.HooksNotInConfig)
+			}
+		})
+	}
+}
+
+func TestBdHookPatternMatching(t *testing.T) {
+	tests := []struct {
+		content string
+		matches bool
+	}{
+		{"bd hooks run pre-commit", true},
+		{"bd  hooks  run pre-commit", true},
+		{"bd hooks run post-merge", true},
+		{`bd hooks run pre-push "$@"`, true},
+		{"if command -v bd; then bd hooks run pre-commit; fi", true},
+		{"# bd hooks run is recommended", true},
+		// Word boundary tests - should NOT match partial words
+		{"kbd hooks runner", false}, // 'kbd' contains 'bd' but is different word
+		{"bd_hooks_run", false},     // underscores make different tokens
+		{"bd sync", false},
+		{"bd export", false},
+		{".beads/", false},
+		{"eslint .", false},
+		{"echo hello", false},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.content, func(t *testing.T) {
+			if got := bdHookPattern.MatchString(tt.content); got != tt.matches {
+				t.Errorf("bdHookPattern.MatchString(%q) = %v, want %v", tt.content, got, tt.matches)
+			}
+		})
+	}
+}
+
+func TestDetectActiveHookManager(t *testing.T) {
+	tests := []struct {
+		name        string
+		hookContent string
+		expected    string
+	}{
+		{
+			name:        "lefthook signature",
+			hookContent: "#!/bin/sh\n# lefthook\nexec lefthook run pre-commit\n",
+			expected:    "lefthook",
+		},
+		{
+			name:        "husky signature",
+			hookContent: "#!/bin/sh\n. \"$(dirname \"$0\")/_/husky.sh\"\nnpm test\n",
+			expected:    "husky",
+		},
+		{
+			name:        "pre-commit framework signature",
+			hookContent: "#!/usr/bin/env bash\n# PRE_COMMIT hook\npre-commit run --all-files\n",
+			expected:    "pre-commit",
+		},
+		{
+			name:        "simple-git-hooks signature",
+			hookContent: "#!/bin/sh\n# simple-git-hooks\nnpm run lint\n",
+			expected:    "simple-git-hooks",
+		},
+		{
+			name:        "no manager signature",
+			hookContent: "#!/bin/sh\necho 'custom hook'\n",
+			expected:    "",
+		},
+		{
+			name:        "empty hook",
+			hookContent: "",
+			expected:    "",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			dir := t.TempDir()
+
+			// Initialize real git repo
+			cmd := exec.Command("git", "init")
+			cmd.Dir = dir
+			if err := cmd.Run(); err != nil {
+				t.Fatalf("failed to init git repo: %v", err)
+			}
+
+			// Write hook file
+			if tt.hookContent != "" {
+				hooksDir := filepath.Join(dir, ".git", "hooks")
+				hookPath := filepath.Join(hooksDir, "pre-commit")
+				if err := os.WriteFile(hookPath, []byte(tt.hookContent), 0755); err != nil {
+					t.Fatalf("failed to write hook: %v", err)
+				}
+			}
+
+			result := DetectActiveHookManager(dir)
+			if result != tt.expected {
+				t.Errorf("DetectActiveHookManager() = %q, want %q", result, tt.expected)
+			}
+		})
+	}
+}
+
+func TestDetectActiveHookManager_CustomHooksPath(t *testing.T) {
+	dir := t.TempDir()
+
+	// Initialize real git repo
+	cmd := exec.Command("git", "init")
+	cmd.Dir = dir
+	if err := cmd.Run(); err != nil {
+		t.Fatalf("failed to init git repo: %v", err)
+	}
+
+	// Create custom hooks directory outside .git
+	customHooksDir := filepath.Join(dir, "my-hooks")
+	if err := os.MkdirAll(customHooksDir, 0755); err != nil {
+		t.Fatalf("failed to create custom hooks dir: %v", err)
+	}
+
+	// Write hook in custom location with lefthook signature
+	hookContent := "#!/bin/sh\n# lefthook\nexec lefthook run pre-commit\n"
+	if err := os.WriteFile(filepath.Join(customHooksDir, "pre-commit"), []byte(hookContent), 0755); err != nil {
+		t.Fatalf("failed to write hook: %v", err)
+	}
+
+	// Set core.hooksPath via git config
+	configCmd := exec.Command("git", "config", "core.hooksPath", "my-hooks")
+	configCmd.Dir = dir
+	if err := configCmd.Run(); err != nil {
+		t.Fatalf("failed to set core.hooksPath: %v", err)
+	}
+
+	result := DetectActiveHookManager(dir)
+	if result != "lefthook" {
+		t.Errorf("DetectActiveHookManager() with core.hooksPath = %q, want %q", result, "lefthook")
+	}
+}
+
+func TestHasBdInCommands(t *testing.T) {
+	tests := []struct {
+		name     string
+		section  interface{}
+		expected bool
+	}{
+		{
+			name: "bd hooks run in commands",
+			section: map[string]interface{}{
+				"commands": map[string]interface{}{
+					"bd": map[string]interface{}{
+						"run": "bd hooks run pre-commit",
+					},
+				},
+			},
+			expected: true,
+		},
+		{
+			name: "no bd in commands",
+			section: map[string]interface{}{
+				"commands": map[string]interface{}{
+					"lint": map[string]interface{}{
+						"run": "eslint .",
+					},
+				},
+			},
+			expected: false,
+		},
+		{
+			name: "bd mentioned in comment not run field",
+			section: map[string]interface{}{
+				"commands": map[string]interface{}{
+					"lint": map[string]interface{}{
+						"run":  "eslint .",
+						"tags": "bd hooks run should be added",
+					},
+				},
+			},
+			expected: false,
+		},
+		{
+			name:     "nil section",
+			section:  nil,
+			expected: false,
+		},
+		{
+			name:     "non-map section",
+			section:  "string value",
+			expected: false,
+		},
+		{
+			name: "no commands key",
+			section: map[string]interface{}{
+				"parallel": true,
+			},
+			expected: false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			result := hasBdInCommands(tt.section)
+			if result != tt.expected {
+				t.Errorf("hasBdInCommands() = %v, want %v", result, tt.expected)
+			}
+		})
+	}
+}
+
+// slicesEqual compares two string slices for equality (order-insensitive)
+func slicesEqual(a, b []string) bool {
+	if len(a) != len(b) {
+		return false
+	}
+	aMap := make(map[string]bool)
+	for _, v := range a {
+		aMap[v] = true
+	}
+	for _, v := range b {
+		if !aMap[v] {
+			return false
+		}
+	}
+	return true
+}
+
+func TestCheckExternalHookManagerIntegration(t *testing.T) {
+	tests := []struct {
+		name             string
+		setup            func(dir string) error
+		expectNil        bool
+		expectManager    string
+		expectConfigured bool
+	}{
+		{
+			name: "no managers",
+			setup: func(dir string) error {
+				return nil
+			},
+			expectNil: true,
+		},
+		{
+			name: "lefthook with bd integration",
+			setup: func(dir string) error {
+				config := `pre-commit:
+  commands:
+    bd:
+      run: bd hooks run pre-commit
+`
+				return os.WriteFile(filepath.Join(dir, "lefthook.yml"), []byte(config), 0644)
+			},
+			expectNil:        false,
+			expectManager:    "lefthook",
+			expectConfigured: true,
+		},
+		{
+			name: "husky with bd integration",
+			setup: func(dir string) error {
+				huskyDir := filepath.Join(dir, ".husky")
+				if err := os.MkdirAll(huskyDir, 0755); err != nil {
+					return err
+				}
+				return os.WriteFile(filepath.Join(huskyDir, "pre-commit"), []byte("#!/bin/sh\nbd hooks run pre-commit\n"), 0755)
+			},
+			expectNil:        false,
+			expectManager:    "husky",
+			expectConfigured: true,
+		},
+		{
+			name: "unsupported manager (pre-commit framework)",
+			setup: func(dir string) error {
+				return os.WriteFile(filepath.Join(dir, ".pre-commit-config.yaml"), []byte("repos:\n"), 0644)
+			},
+			expectNil:        false,
+			expectManager:    "pre-commit",
+			expectConfigured: false,
+		},
+		{
+			name: "lefthook without bd",
+			setup: func(dir string) error {
+				config := `pre-commit:
+  commands:
+    lint:
+      run: eslint .
+`
+				return os.WriteFile(filepath.Join(dir, "lefthook.yml"), []byte(config), 0644)
+			},
+			expectNil:        false,
+			expectManager:    "lefthook",
+			expectConfigured: false,
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			dir := t.TempDir()
+			if err := tt.setup(dir); err != nil {
+				t.Fatalf("setup failed: %v", err)
+			}
+
+			result := CheckExternalHookManagerIntegration(dir)
+
+			if tt.expectNil {
+				if result != nil {
+					t.Errorf("expected nil, got %+v", result)
+				}
+				return
+			}
+
+			if result == nil {
+				t.Fatal("expected non-nil result")
+			}
+
+			if result.Manager != tt.expectManager {
+				t.Errorf("Manager: expected %q, got %q", tt.expectManager, result.Manager)
+			}
+
+			if result.Configured != tt.expectConfigured {
+				t.Errorf("Configured: expected %v, got %v", tt.expectConfigured, result.Configured)
+			}
+		})
+	}
+}
+
+func TestMultipleManagersDetected(t *testing.T) {
+	tests := []struct {
+		name          string
+		setup         func(dir string) error
+		expectManager string
+	}{
+		{
+			name: "lefthook and husky both present - lefthook wins by priority",
+			setup: func(dir string) error {
+				// Create lefthook config
+				config := `pre-commit:
+  commands:
+    bd:
+      run: bd hooks run pre-commit
+`
+				if err := os.WriteFile(filepath.Join(dir, "lefthook.yml"), []byte(config), 0644); err != nil {
+					return err
+				}
+				// Create husky directory
+				huskyDir := filepath.Join(dir, ".husky")
+				if err := os.MkdirAll(huskyDir, 0755); err != nil {
+					return err
+				}
+				return os.WriteFile(filepath.Join(huskyDir, "pre-commit"), []byte("#!/bin/sh\nbd hooks run pre-commit\n"), 0755)
+			},
+			expectManager: "lefthook",
+		},
+		{
+			name: "husky only",
+			setup: func(dir string) error {
+				huskyDir := filepath.Join(dir, ".husky")
+				if err := os.MkdirAll(huskyDir, 0755); err != nil {
+					return err
+				}
+				return os.WriteFile(filepath.Join(huskyDir, "pre-commit"), []byte("#!/bin/sh\nbd hooks run pre-commit\n"), 0755)
+			},
+			expectManager: "husky",
+		},
+		{
+			name: "multiple unsupported managers",
+			setup: func(dir string) error {
+				// pre-commit and overcommit
+				if err := os.WriteFile(filepath.Join(dir, ".pre-commit-config.yaml"), []byte("repos:\n"), 0644); err != nil {
+					return err
+				}
+				return os.WriteFile(filepath.Join(dir, ".overcommit.yml"), []byte("PreCommit:\n"), 0644)
+			},
+			expectManager: "pre-commit, overcommit", // Falls through to basic status
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			dir := t.TempDir()
+			if err := tt.setup(dir); err != nil {
+				t.Fatalf("setup failed: %v", err)
+			}
+
+			result := CheckExternalHookManagerIntegration(dir)
+			if result == nil {
+				t.Fatal("expected non-nil result")
+			}
+
+			if result.Manager != tt.expectManager {
+				t.Errorf("Manager: expected %q, got %q", tt.expectManager, result.Manager)
+			}
+		})
+	}
+}
+
+func TestManagerNames(t *testing.T) {
+	tests := []struct {
+		managers []ExternalHookManager
+		expected string
+	}{
+		{nil, ""},
+		{[]ExternalHookManager{}, ""},
+		{[]ExternalHookManager{{Name: "lefthook"}}, "lefthook"},
+		{[]ExternalHookManager{{Name: "lefthook"}, {Name: "husky"}}, "lefthook, husky"},
+		{[]ExternalHookManager{{Name: "a"}, {Name: "b"}, {Name: "c"}}, "a, b, c"},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.expected, func(t *testing.T) {
+			result := ManagerNames(tt.managers)
+			if result != tt.expected {
+				t.Errorf("ManagerNames() = %q, want %q", result, tt.expected)
+			}
+		})
+	}
+}
+
+func TestCheckManagerBdIntegration(t *testing.T) {
+	tests := []struct {
+		name          string
+		managerName   string
+		setup         func(dir string) error
+		expectNil     bool
+		expectManager string
+	}{
+		{
+			name:        "unknown manager returns nil",
+			managerName: "unknown-manager",
+			setup:       func(dir string) error { return nil },
+			expectNil:   true,
+		},
+		{
+			name:        "lefthook integration",
+			managerName: "lefthook",
+			setup: func(dir string) error {
+				return os.WriteFile(filepath.Join(dir, "lefthook.yml"), []byte("pre-commit:\n  commands:\n    bd:\n      run: bd hooks run pre-commit\n"), 0644)
+			},
+			expectNil:     false,
+			expectManager: "lefthook",
+		},
+		{
+			name:        "husky integration",
+			managerName: "husky",
+			setup: func(dir string) error {
+				huskyDir := filepath.Join(dir, ".husky")
+				if err := os.MkdirAll(huskyDir, 0755); err != nil {
+					return err
+				}
+				return os.WriteFile(filepath.Join(huskyDir, "pre-commit"), []byte("bd hooks run pre-commit"), 0755)
+			},
+			expectNil:     false,
+			expectManager: "husky",
+		},
+	}
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			dir := t.TempDir()
+			if err := tt.setup(dir); err != nil {
+				t.Fatalf("setup failed: %v", err)
+			}
+
+			result := checkManagerBdIntegration(tt.managerName, dir)
+
+			if tt.expectNil {
+				if result != nil {
+					t.Errorf("expected nil, got %+v", result)
+				}
+				return
+			}
+
+			if result == nil {
+				t.Fatal("expected non-nil result")
+			}
+
+			if result.Manager != tt.expectManager {
+				t.Errorf("Manager: expected %q, got %q", tt.expectManager, result.Manager)
+			}
+		})
+	}
+}
+
+func TestDetectExternalHookManagers_MultiplePresentInOrder(t *testing.T) {
+	dir := t.TempDir()
+
+	// Create configs for multiple managers
+	// lefthook (priority 0)
+	if err := os.WriteFile(filepath.Join(dir, "lefthook.yml"), []byte("pre-commit:\n"), 0644); err != nil {
+		t.Fatal(err)
+	}
+	// husky (priority 1)
+	if err := os.MkdirAll(filepath.Join(dir, ".husky"), 0755); err != nil {
+		t.Fatal(err)
+	}
+	// pre-commit (priority 2)
+	if err := os.WriteFile(filepath.Join(dir, ".pre-commit-config.yaml"), []byte("repos:\n"), 0644); err != nil {
+		t.Fatal(err)
+	}
+
+	managers := DetectExternalHookManagers(dir)
+
+	if len(managers) != 3 {
+		t.Fatalf("expected 3 managers, got %d: %v", len(managers), managers)
+	}
+
+	// Verify order matches priority
+	expectedOrder := []string{"lefthook", "husky", "pre-commit"}
+	for i, exp := range expectedOrder {
+		if managers[i].Name != exp {
+			t.Errorf("managers[%d]: expected %q, got %q", i, exp, managers[i].Name)
+		}
+	}
+}
diff --git a/cmd/bd/doctor/git.go b/cmd/bd/doctor/git.go
index ca96edd0..b328b9b2 100644
--- a/cmd/bd/doctor/git.go
+++ b/cmd/bd/doctor/git.go
@@ -16,6 +16,11 @@ import (
 	"github.com/steveyegge/beads/internal/syncbranch"
 )
 
+const (
+	hooksExamplesURL = "https://github.com/steveyegge/beads/tree/main/examples/git-hooks"
+	hooksUpgradeURL  = "https://github.com/steveyegge/beads/issues/615"
+)
+
 // CheckGitHooks verifies that recommended git hooks are installed.
 func CheckGitHooks() DoctorCheck {
 	// Check if we're in a git repository using worktree-aware detection
@@ -48,6 +53,51 @@ func CheckGitHooks() DoctorCheck {
 		}
 	}
 
+	// Get repo root for external manager detection
+	repoRoot := filepath.Dir(gitDir)
+	if filepath.Base(gitDir) != ".git" {
+		// Worktree case - gitDir might be .git file content
+		if cwd, err := os.Getwd(); err == nil {
+			repoRoot = cwd
+		}
+	}
+
+	// Check for external hook managers (lefthook, husky, etc.)
+	externalManagers := fix.DetectExternalHookManagers(repoRoot)
+	if len(externalManagers) > 0 {
+		// External manager detected - check if it's configured to call bd
+		integration := fix.CheckExternalHookManagerIntegration(repoRoot)
+		if integration != nil && integration.Configured {
+			// Check if any hooks are missing bd integration
+			if len(integration.HooksWithoutBd) > 0 {
+				return DoctorCheck{
+					Name:    "Git Hooks",
+					Status:  StatusWarning,
+					Message: fmt.Sprintf("%s hooks not calling bd", integration.Manager),
+					Detail:  fmt.Sprintf("Missing bd: %s", strings.Join(integration.HooksWithoutBd, ", ")),
+					Fix:     "Add or upgrade to 'bd hooks run <hook>'. See " + hooksUpgradeURL,
+				}
+			}
+
+			// All hooks calling bd - success
+			return DoctorCheck{
+				Name:    "Git Hooks",
+				Status:  StatusOK,
+				Message: fmt.Sprintf("All hooks via %s", integration.Manager),
+				Detail:  fmt.Sprintf("bd hooks run: %s", strings.Join(integration.HooksWithBd, ", ")),
+			}
+		} else {
+			// External manager exists but doesn't call bd at all
+			return DoctorCheck{
+				Name:    "Git Hooks",
+				Status:  StatusWarning,
+				Message: fmt.Sprintf("%s not calling bd", fix.ManagerNames(externalManagers)),
+				Detail:  "Configure hooks to call bd commands",
+				Fix:     "Add or upgrade to 'bd hooks run <hook>'. See " + hooksUpgradeURL,
+			}
+		}
+	}
+
 	if len(missingHooks) == 0 {
 		return DoctorCheck{
 			Name:    "Git Hooks",
@@ -57,7 +107,7 @@ func CheckGitHooks() DoctorCheck {
 		}
 	}
 
-	hookInstallMsg := "Install hooks with 'bd hooks install'. See https://github.com/steveyegge/beads/tree/main/examples/git-hooks for installation instructions"
+	hookInstallMsg := "Install hooks with 'bd hooks install'. See " + hooksExamplesURL
 
 	if len(installedHooks) > 0 {
 		return DoctorCheck{
@@ -293,7 +343,58 @@ func CheckSyncBranchHookCompatibility(path string) DoctorCheck {
 	// Check if this is a bd hook and extract version
 	hookStr := string(hookContent)
 	if !strings.Contains(hookStr, "bd-hooks-version:") {
-		// Not a bd hook - can't determine compatibility
+		// Not a bd hook - check if it's an external hook manager
+		externalManagers := fix.DetectExternalHookManagers(path)
+		if len(externalManagers) > 0 {
+			names := fix.ManagerNames(externalManagers)
+
+			// Check if external manager has bd integration
+			integration := fix.CheckExternalHookManagerIntegration(path)
+			if integration != nil && integration.Configured {
+				// Has bd integration - check if pre-push is covered
+				hasPrepush := false
+				for _, h := range integration.HooksWithBd {
+					if h == "pre-push" {
+						hasPrepush = true
+						break
+					}
+				}
+
+				if hasPrepush {
+					var detail string
+					// Only report hooks that ARE in config but lack bd integration
+					if len(integration.HooksWithoutBd) > 0 {
+						detail = fmt.Sprintf("Hooks without bd: %s", strings.Join(integration.HooksWithoutBd, ", "))
+					}
+					return DoctorCheck{
+						Name:    "Sync Branch Hook Compatibility",
+						Status:  StatusOK,
+						Message: fmt.Sprintf("Managed by %s with bd integration", integration.Manager),
+						Detail:  detail,
+					}
+				}
+
+				// Has bd integration but missing pre-push
+				return DoctorCheck{
+					Name:    "Sync Branch Hook Compatibility",
+					Status:  StatusWarning,
+					Message: fmt.Sprintf("Managed by %s (missing pre-push bd integration)", integration.Manager),
+					Detail:  "pre-push hook needs 'bd hooks run pre-push' for sync-branch",
+					Fix:     fmt.Sprintf("Add or upgrade to 'bd hooks run pre-push' in %s. See %s", integration.Manager, hooksExamplesURL),
+				}
+			}
+
+			// External manager detected but no bd integration found
+			return DoctorCheck{
+				Name:    "Sync Branch Hook Compatibility",
+				Status:  StatusWarning,
+				Message: fmt.Sprintf("Managed by %s (no bd integration detected)", names),
+				Detail:  fmt.Sprintf("Pre-push hook managed by %s but no 'bd hooks run' found", names),
+				Fix:     fmt.Sprintf("Add or upgrade to 'bd hooks run <hook>' in %s. See %s", names, hooksExamplesURL),
+			}
+		}
+
+		// No external manager - truly custom hook
 		return DoctorCheck{
 			Name:    "Sync Branch Hook Compatibility",
 			Status:  StatusWarning,