diff --git a/cmd/bd/init.go b/cmd/bd/init.go
index 51e9b619..7150b3a7 100644
--- a/cmd/bd/init.go
+++ b/cmd/bd/init.go
@@ -388,8 +388,8 @@ With --stealth: configures global git settings for invisible beads usage:
 		}
 
 		// Check if we're in a git repo and hooks aren't installed
-		// Install by default unless --skip-hooks is passed
-		if !skipHooks && isGitRepo() && !hooksInstalled() {
+		// Install by default unless --skip-hooks is passed or no-install-hooks config is set
+		if !skipHooks && !config.GetBool("no-install-hooks") && isGitRepo() && !hooksInstalled() {
 			if err := installGitHooks(); err != nil && !quiet {
 				yellow := color.New(color.FgYellow).SprintFunc()
 				fmt.Fprintf(os.Stderr, "\n%s Failed to install git hooks: %v\n", yellow("⚠"), err)
diff --git a/cmd/bd/init_test.go b/cmd/bd/init_test.go
index c91ceabf..daa3ddb4 100644
--- a/cmd/bd/init_test.go
+++ b/cmd/bd/init_test.go
@@ -1041,3 +1041,188 @@ func TestSetupClaudeSettings_NoExistingFile(t *testing.T) {
 		t.Error("File should contain bd onboard prompt")
 	}
 }
+
+// TestInitSkipHooksWithEnvVar verifies BD_NO_INSTALL_HOOKS=1 prevents hook installation
+func TestInitSkipHooksWithEnvVar(t *testing.T) {
+	// Reset global state
+	origDBPath := dbPath
+	defer func() { dbPath = origDBPath }()
+	dbPath = ""
+
+	tmpDir := t.TempDir()
+	t.Chdir(tmpDir)
+
+	// Initialize git repo first (hooks only install in git repos)
+	if err := runCommandInDir(tmpDir, "git", "init"); err != nil {
+		t.Fatalf("Failed to init git: %v", err)
+	}
+
+	// Set environment variable to skip hooks
+	os.Setenv("BD_NO_INSTALL_HOOKS", "1")
+	defer os.Unsetenv("BD_NO_INSTALL_HOOKS")
+
+	// Run bd init
+	rootCmd.SetArgs([]string{"init", "--prefix", "test", "--quiet"})
+	if err := rootCmd.Execute(); err != nil {
+		t.Fatalf("Init failed: %v", err)
+	}
+
+	// Verify .beads directory was created
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
+		t.Error(".beads directory was not created")
+	}
+
+	// Verify git hooks were NOT installed
+	preCommitHook := filepath.Join(tmpDir, ".git", "hooks", "pre-commit")
+	if _, err := os.Stat(preCommitHook); err == nil {
+		t.Error("pre-commit hook should NOT be installed when BD_NO_INSTALL_HOOKS=1")
+	}
+
+	postMergeHook := filepath.Join(tmpDir, ".git", "hooks", "post-merge")
+	if _, err := os.Stat(postMergeHook); err == nil {
+		t.Error("post-merge hook should NOT be installed when BD_NO_INSTALL_HOOKS=1")
+	}
+}
+
+// TestInitSkipHooksWithConfigFile verifies no-install-hooks: true in config prevents hook installation
+func TestInitSkipHooksWithConfigFile(t *testing.T) {
+	// Reset global state
+	origDBPath := dbPath
+	defer func() { dbPath = origDBPath }()
+	dbPath = ""
+
+	tmpDir := t.TempDir()
+	t.Chdir(tmpDir)
+
+	// Initialize git repo first
+	if err := runCommandInDir(tmpDir, "git", "init"); err != nil {
+		t.Fatalf("Failed to init git: %v", err)
+	}
+
+	// Create global config directory with no-install-hooks: true
+	configDir, err := os.UserConfigDir()
+	if err != nil {
+		t.Fatalf("Failed to get user config dir: %v", err)
+	}
+	bdConfigDir := filepath.Join(configDir, "bd")
+	if err := os.MkdirAll(bdConfigDir, 0755); err != nil {
+		t.Fatalf("Failed to create config dir: %v", err)
+	}
+	configPath := filepath.Join(bdConfigDir, "config.yaml")
+
+	// Backup existing config if present
+	existingConfig, existingErr := os.ReadFile(configPath)
+	defer func() {
+		if existingErr == nil {
+			os.WriteFile(configPath, existingConfig, 0644)
+		} else {
+			os.Remove(configPath)
+		}
+	}()
+
+	// Write test config
+	if err := os.WriteFile(configPath, []byte("no-install-hooks: true\n"), 0644); err != nil {
+		t.Fatalf("Failed to write config: %v", err)
+	}
+
+	// Run bd init
+	rootCmd.SetArgs([]string{"init", "--prefix", "test", "--quiet"})
+	if err := rootCmd.Execute(); err != nil {
+		t.Fatalf("Init failed: %v", err)
+	}
+
+	// Verify .beads directory was created
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
+		t.Error(".beads directory was not created")
+	}
+
+	// Verify git hooks were NOT installed
+	preCommitHook := filepath.Join(tmpDir, ".git", "hooks", "pre-commit")
+	if _, err := os.Stat(preCommitHook); err == nil {
+		t.Error("pre-commit hook should NOT be installed when no-install-hooks: true in config")
+	}
+}
+
+// TestInitSkipHooksFlag verifies --skip-hooks flag still works (backward compat)
+func TestInitSkipHooksFlag(t *testing.T) {
+	// Reset global state
+	origDBPath := dbPath
+	defer func() { dbPath = origDBPath }()
+	dbPath = ""
+
+	// Reset Cobra flags
+	initCmd.Flags().Set("skip-hooks", "false")
+
+	tmpDir := t.TempDir()
+	t.Chdir(tmpDir)
+
+	// Initialize git repo first
+	if err := runCommandInDir(tmpDir, "git", "init"); err != nil {
+		t.Fatalf("Failed to init git: %v", err)
+	}
+
+	// Run bd init with --skip-hooks
+	rootCmd.SetArgs([]string{"init", "--prefix", "test", "--quiet", "--skip-hooks"})
+	if err := rootCmd.Execute(); err != nil {
+		t.Fatalf("Init failed: %v", err)
+	}
+
+	// Verify .beads directory was created
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
+		t.Error(".beads directory was not created")
+	}
+
+	// Verify git hooks were NOT installed
+	preCommitHook := filepath.Join(tmpDir, ".git", "hooks", "pre-commit")
+	if _, err := os.Stat(preCommitHook); err == nil {
+		t.Error("pre-commit hook should NOT be installed when --skip-hooks is passed")
+	}
+}
+
+// TestInitDefaultInstallsHooks verifies default behavior installs hooks
+func TestInitDefaultInstallsHooks(t *testing.T) {
+	// Reset global state
+	origDBPath := dbPath
+	defer func() { dbPath = origDBPath }()
+	dbPath = ""
+
+	// Reset Cobra flags
+	initCmd.Flags().Set("skip-hooks", "false")
+
+	// Clear any env var that might affect hooks
+	os.Unsetenv("BD_NO_INSTALL_HOOKS")
+
+	tmpDir := t.TempDir()
+	t.Chdir(tmpDir)
+
+	// Initialize git repo first
+	if err := runCommandInDir(tmpDir, "git", "init"); err != nil {
+		t.Fatalf("Failed to init git: %v", err)
+	}
+
+	// Run bd init without any hook-skipping options
+	rootCmd.SetArgs([]string{"init", "--prefix", "test", "--quiet"})
+	if err := rootCmd.Execute(); err != nil {
+		t.Fatalf("Init failed: %v", err)
+	}
+
+	// Verify .beads directory was created
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	if _, err := os.Stat(beadsDir); os.IsNotExist(err) {
+		t.Error(".beads directory was not created")
+	}
+
+	// Verify git hooks WERE installed (default behavior)
+	preCommitHook := filepath.Join(tmpDir, ".git", "hooks", "pre-commit")
+	if _, err := os.Stat(preCommitHook); os.IsNotExist(err) {
+		t.Error("pre-commit hook SHOULD be installed by default")
+	}
+
+	postMergeHook := filepath.Join(tmpDir, ".git", "hooks", "post-merge")
+	if _, err := os.Stat(postMergeHook); os.IsNotExist(err) {
+		t.Error("post-merge hook SHOULD be installed by default")
+	}
+}
diff --git a/docs/CONFIG.md b/docs/CONFIG.md
index 4898fc33..631cdfaa 100644
--- a/docs/CONFIG.md
+++ b/docs/CONFIG.md
@@ -34,6 +34,7 @@ Tool-level settings you can configure:
 | `no-daemon` | `--no-daemon` | `BD_NO_DAEMON` | `false` | Force direct mode, bypass daemon |
 | `no-auto-flush` | `--no-auto-flush` | `BD_NO_AUTO_FLUSH` | `false` | Disable auto JSONL export |
 | `no-auto-import` | `--no-auto-import` | `BD_NO_AUTO_IMPORT` | `false` | Disable auto JSONL import |
+| `no-install-hooks` | `--skip-hooks` | `BD_NO_INSTALL_HOOKS` | `false` | Skip git hook installation during `bd init` |
 | `db` | `--db` | `BD_DB` | (auto-discover) | Database path |
 | `actor` | `--actor` | `BD_ACTOR` | `$USER` | Actor name for audit trail |
 | `flush-debounce` | - | `BEADS_FLUSH_DEBOUNCE` | `5s` | Debounce time for auto-flush |
@@ -59,6 +60,10 @@ flush-debounce: 10s
 # Auto-start daemon (default true)
 auto-start-daemon: true
 
+# Disable git hook installation during bd init
+# (useful if you manage hooks with pre-commit, husky, etc.)
+no-install-hooks: true
+
 # Daemon log rotation settings
 daemon-log-max-size: 50      # MB per file (default 50)
 daemon-log-max-backups: 7    # Number of old logs to keep (default 7)
diff --git a/docs/GIT_INTEGRATION.md b/docs/GIT_INTEGRATION.md
index 3926a5f0..6332439b 100644
--- a/docs/GIT_INTEGRATION.md
+++ b/docs/GIT_INTEGRATION.md
@@ -251,11 +251,33 @@ See [PROTECTED_BRANCHES.md](PROTECTED_BRANCHES.md) for complete setup guide, tro
 
 ### Installation
 
+Git hooks are installed automatically during `bd init`. To install manually:
+
 ```bash
 # One-time setup in each beads workspace
 ./examples/git-hooks/install.sh
 ```
 
+### Disabling Hook Installation
+
+If you prefer to manage git hooks separately (e.g., using pre-commit, husky, or your own hook manager), you can disable automatic hook installation:
+
+```bash
+# Via command-line flag
+bd init --skip-hooks
+
+# Via environment variable (useful for CI/scripts)
+BD_NO_INSTALL_HOOKS=1 bd init
+
+# Via global config (~/.config/bd/config.yaml)
+no-install-hooks: true
+
+# Via project config (.beads/config.yaml)
+no-install-hooks: true
+```
+
+**Precedence:** `--skip-hooks` flag > `BD_NO_INSTALL_HOOKS` env var > config file > default (install hooks)
+
 ### What Gets Installed
 
 **pre-commit hook:**
diff --git a/internal/config/config.go b/internal/config/config.go
index bb82264b..fbb86491 100644
--- a/internal/config/config.go
+++ b/internal/config/config.go
@@ -83,6 +83,7 @@ func Initialize() error {
 	v.SetDefault("db", "")
 	v.SetDefault("actor", "")
 	v.SetDefault("issue-prefix", "")
+	v.SetDefault("no-install-hooks", false)
 	
 	// Additional environment variables (not prefixed with BD_)
 	// These are bound explicitly for backward compatibility