diff --git a/cmd/bd/doctor.go b/cmd/bd/doctor.go
index 3ce7f3c1..09bd2c80 100644
--- a/cmd/bd/doctor.go
+++ b/cmd/bd/doctor.go
@@ -281,6 +281,13 @@ func runDiagnostics(path string) doctorResult {
 		result.OverallOK = false
 	}
 
+	// Check git hooks Dolt compatibility (hooks without Dolt check cause errors)
+	doltHooksCheck := convertWithCategory(doctor.CheckGitHooksDoltCompatibility(path), doctor.CategoryGit)
+	result.Checks = append(result.Checks, doltHooksCheck)
+	if doltHooksCheck.Status == statusError {
+		result.OverallOK = false
+	}
+
 	// If no .beads/, skip remaining checks
 	if installCheck.Status != statusOK {
 		return result
diff --git a/cmd/bd/doctor/git.go b/cmd/bd/doctor/git.go
index 1771ec20..756bb023 100644
--- a/cmd/bd/doctor/git.go
+++ b/cmd/bd/doctor/git.go
@@ -13,6 +13,7 @@ import (
 	_ "github.com/ncruces/go-sqlite3/driver"
 	_ "github.com/ncruces/go-sqlite3/embed"
 	"github.com/steveyegge/beads/cmd/bd/doctor/fix"
+	"github.com/steveyegge/beads/internal/configfile"
 	"github.com/steveyegge/beads/internal/git"
 	"github.com/steveyegge/beads/internal/storage"
 	"github.com/steveyegge/beads/internal/syncbranch"
@@ -760,6 +761,74 @@ func CheckSyncBranchHealth(path string) DoctorCheck {
 	}
 }
 
+// CheckGitHooksDoltCompatibility checks if installed git hooks are compatible with Dolt backend.
+// Hooks installed before Dolt support was added don't have the backend check and will
+// fail with confusing errors on git pull/commit.
+func CheckGitHooksDoltCompatibility(path string) DoctorCheck {
+	backend, beadsDir := getBackendAndBeadsDir(path)
+
+	// Only relevant for Dolt backend
+	if backend != configfile.BackendDolt {
+		return DoctorCheck{
+			Name:    "Git Hooks Dolt Compatibility",
+			Status:  StatusOK,
+			Message: "N/A (not using Dolt backend)",
+		}
+	}
+
+	// Check if we're in a git repository
+	hooksDir, err := git.GetGitHooksDir()
+	if err != nil {
+		return DoctorCheck{
+			Name:    "Git Hooks Dolt Compatibility",
+			Status:  StatusOK,
+			Message: "N/A (not a git repository)",
+		}
+	}
+
+	// Check post-merge hook (most likely to cause issues with Dolt)
+	postMergePath := filepath.Join(hooksDir, "post-merge")
+	content, err := os.ReadFile(postMergePath)
+	if err != nil {
+		// No hook installed - that's fine
+		return DoctorCheck{
+			Name:    "Git Hooks Dolt Compatibility",
+			Status:  StatusOK,
+			Message: "N/A (no post-merge hook installed)",
+		}
+	}
+
+	contentStr := string(content)
+
+	// Check if it's a bd hook
+	if !strings.Contains(contentStr, bdInlineHookMarker) && !strings.Contains(contentStr, "bd") {
+		return DoctorCheck{
+			Name:    "Git Hooks Dolt Compatibility",
+			Status:  StatusOK,
+			Message: "N/A (not a bd hook)",
+		}
+	}
+
+	// Check if it has the Dolt backend skip logic
+	if strings.Contains(contentStr, `"backend"`) && strings.Contains(contentStr, `"dolt"`) {
+		return DoctorCheck{
+			Name:    "Git Hooks Dolt Compatibility",
+			Status:  StatusOK,
+			Message: "Hooks have Dolt backend check",
+		}
+	}
+
+	// Hook exists but lacks Dolt check - this will cause errors
+	_ = beadsDir // silence unused warning
+	return DoctorCheck{
+		Name:    "Git Hooks Dolt Compatibility",
+		Status:  StatusError,
+		Message: "Git hooks incompatible with Dolt backend",
+		Detail:  "Installed hooks attempt JSONL sync which fails with Dolt. This causes errors on git pull/commit.",
+		Fix:     "Run 'bd hooks install --force' to update hooks for Dolt compatibility",
+	}
+}
+
 // FixGitHooks fixes missing or broken git hooks by calling bd hooks install.
 func FixGitHooks(path string) error {
 	return fix.GitHooks(path)
diff --git a/cmd/bd/migrate_dolt.go b/cmd/bd/migrate_dolt.go
index b4409d2b..834c208f 100644
--- a/cmd/bd/migrate_dolt.go
+++ b/cmd/bd/migrate_dolt.go
@@ -146,10 +146,44 @@ func handleToDoltMigration(dryRun bool, autoYes bool) {
 
 	printSuccess("Updated metadata.json to use Dolt backend")
 
+	// Check if git hooks need updating for Dolt compatibility
+	if hooksNeedDoltUpdate(beadsDir) {
+		printWarning("Git hooks need updating for Dolt backend")
+		if !jsonOutput {
+			fmt.Println("  The pre-commit and post-merge hooks use JSONL sync which doesn't apply to Dolt.")
+			fmt.Println("  Run 'bd hooks install --force' to update them.")
+		}
+	}
+
 	// Final status
 	printFinalStatus("dolt", imported, skipped, backupPath, doltPath, sqlitePath, true)
 }
 
+// hooksNeedDoltUpdate checks if installed git hooks lack the Dolt backend skip logic.
+func hooksNeedDoltUpdate(beadsDir string) bool {
+	// Find git hooks directory
+	repoRoot := filepath.Dir(beadsDir)
+	hooksDir := filepath.Join(repoRoot, ".git", "hooks")
+
+	// Check post-merge hook (most likely to cause issues)
+	postMergePath := filepath.Join(hooksDir, "post-merge")
+	content, err := os.ReadFile(postMergePath)
+	if err != nil {
+		return false // No hook installed
+	}
+
+	// Check if it's a bd hook and lacks the Dolt skip logic
+	contentStr := string(content)
+	if !strings.Contains(contentStr, "bd") {
+		return false // Not a bd hook
+	}
+	if strings.Contains(contentStr, `"backend"`) && strings.Contains(contentStr, `"dolt"`) {
+		return false // Already has Dolt check
+	}
+
+	return true // bd hook without Dolt check
+}
+
 // handleToSQLiteMigration migrates from Dolt to SQLite backend (escape hatch).
 func handleToSQLiteMigration(dryRun bool, autoYes bool) {
 	ctx := context.Background()