diff --git a/cmd/bd/init.go b/cmd/bd/init.go
index 17fc65cd..ad2861fa 100644
--- a/cmd/bd/init.go
+++ b/cmd/bd/init.go
@@ -353,7 +353,6 @@ With --no-db: creates .beads/ directory and issues.jsonl file instead of SQLite
 
 		green := color.New(color.FgGreen).SprintFunc()
 		cyan := color.New(color.FgCyan).SprintFunc()
-		yellow := color.New(color.FgYellow).SprintFunc()
 
 		fmt.Printf("\n%s bd initialized successfully!\n\n", green("✓"))
 		fmt.Printf("  Database: %s\n", cyan(initDBPath))
diff --git a/cmd/bd/sync.go b/cmd/bd/sync.go
index 0d5f8869..34eeeb46 100644
--- a/cmd/bd/sync.go
+++ b/cmd/bd/sync.go
@@ -204,19 +204,49 @@ Use --merge to merge the sync branch back to main branch.`,
 
 				fmt.Println("→ Pulling from remote...")
 				if err := gitPull(ctx); err != nil {
-					fmt.Fprintf(os.Stderr, "Error pulling: %v\n", err)
+					// Check if it's a rebase conflict on beads.jsonl that we can auto-resolve
+					if isInRebase() && hasJSONLConflict() {
+						fmt.Println("→ Auto-resolving JSONL merge conflict...")
 
-					// Check if this looks like a merge driver failure
-					errStr := err.Error()
-					if strings.Contains(errStr, "merge driver") ||
-					   strings.Contains(errStr, "no such file or directory") ||
-					   strings.Contains(errStr, "MERGE DRIVER INVOKED") {
-						fmt.Fprintf(os.Stderr, "\nThis may be caused by an incorrect merge driver configuration.\n")
-						fmt.Fprintf(os.Stderr, "Fix: bd doctor --fix\n\n")
+						// Export clean JSONL from DB (database is source of truth)
+						if exportErr := exportToJSONL(ctx, jsonlPath); exportErr != nil {
+							fmt.Fprintf(os.Stderr, "Error: failed to export for conflict resolution: %v\n", exportErr)
+							fmt.Fprintf(os.Stderr, "Hint: resolve conflicts manually and run 'bd import' then 'bd sync' again\n")
+							os.Exit(1)
+						}
+
+						// Mark conflict as resolved
+						addCmd := exec.CommandContext(ctx, "git", "add", jsonlPath)
+						if addErr := addCmd.Run(); addErr != nil {
+							fmt.Fprintf(os.Stderr, "Error: failed to mark conflict resolved: %v\n", addErr)
+							fmt.Fprintf(os.Stderr, "Hint: resolve conflicts manually and run 'bd import' then 'bd sync' again\n")
+							os.Exit(1)
+						}
+
+						// Continue rebase
+						if continueErr := runGitRebaseContinue(ctx); continueErr != nil {
+							fmt.Fprintf(os.Stderr, "Error: failed to continue rebase: %v\n", continueErr)
+							fmt.Fprintf(os.Stderr, "Hint: resolve conflicts manually and run 'bd import' then 'bd sync' again\n")
+							os.Exit(1)
+						}
+
+						fmt.Println("✓ Auto-resolved JSONL conflict")
+					} else {
+						// Not an auto-resolvable conflict, fail with original error
+						fmt.Fprintf(os.Stderr, "Error pulling: %v\n", err)
+
+						// Check if this looks like a merge driver failure
+						errStr := err.Error()
+						if strings.Contains(errStr, "merge driver") ||
+						   strings.Contains(errStr, "no such file or directory") ||
+						   strings.Contains(errStr, "MERGE DRIVER INVOKED") {
+							fmt.Fprintf(os.Stderr, "\nThis may be caused by an incorrect merge driver configuration.\n")
+							fmt.Fprintf(os.Stderr, "Fix: bd doctor --fix\n\n")
+						}
+
+						fmt.Fprintf(os.Stderr, "Hint: resolve conflicts manually and run 'bd import' then 'bd sync' again\n")
+						os.Exit(1)
 					}
-
-					fmt.Fprintf(os.Stderr, "Hint: resolve conflicts manually and run 'bd import' then 'bd sync' again\n")
-					os.Exit(1)
 				}
 
 				// Count issues before import for validation
@@ -439,6 +469,64 @@ func hasGitRemote(ctx context.Context) bool {
 	return len(strings.TrimSpace(string(output))) > 0
 }
 
+// isInRebase checks if we're currently in a git rebase state
+func isInRebase() bool {
+	// Check for rebase-merge directory (interactive rebase)
+	if _, err := os.Stat(".git/rebase-merge"); err == nil {
+		return true
+	}
+	// Check for rebase-apply directory (non-interactive rebase)
+	if _, err := os.Stat(".git/rebase-apply"); err == nil {
+		return true
+	}
+	return false
+}
+
+// hasJSONLConflict checks if beads.jsonl has a merge conflict
+// Returns true only if beads.jsonl is the only file in conflict
+func hasJSONLConflict() bool {
+	cmd := exec.Command("git", "status", "--porcelain")
+	out, err := cmd.Output()
+	if err != nil {
+		return false
+	}
+
+	var hasJSONLConflict bool
+	var hasOtherConflict bool
+
+	for _, line := range strings.Split(string(out), "\n") {
+		if len(line) < 3 {
+			continue
+		}
+
+		// Check for unmerged status codes (UU = both modified, AA = both added, etc.)
+		status := line[:2]
+		if status == "UU" || status == "AA" || status == "DD" ||
+		   status == "AU" || status == "UA" || status == "DU" || status == "UD" {
+			filepath := strings.TrimSpace(line[3:])
+
+			if strings.HasSuffix(filepath, "beads.jsonl") {
+				hasJSONLConflict = true
+			} else {
+				hasOtherConflict = true
+			}
+		}
+	}
+
+	// Only return true if ONLY beads.jsonl has a conflict
+	return hasJSONLConflict && !hasOtherConflict
+}
+
+// runGitRebaseContinue continues a rebase after resolving conflicts
+func runGitRebaseContinue(ctx context.Context) error {
+	cmd := exec.CommandContext(ctx, "git", "rebase", "--continue")
+	output, err := cmd.CombinedOutput()
+	if err != nil {
+		return fmt.Errorf("git rebase --continue failed: %w\n%s", err, output)
+	}
+	return nil
+}
+
 // gitPull pulls from the current branch's upstream
 // Returns nil if no remote configured (local-only mode)
 func checkMergeDriverConfig() {
diff --git a/cmd/bd/sync_test.go b/cmd/bd/sync_test.go
index 36bc1844..bf4ff212 100644
--- a/cmd/bd/sync_test.go
+++ b/cmd/bd/sync_test.go
@@ -441,3 +441,169 @@ func TestGetSyncBranch_EnvOverridesDB(t *testing.T) {
 		t.Errorf("getSyncBranch() = %q, want %q (env override)", branch, "env-branch")
 	}
 }
+
+func TestIsInRebase_NotInRebase(t *testing.T) {
+	tmpDir := t.TempDir()
+	originalWd, _ := os.Getwd()
+	defer os.Chdir(originalWd)
+
+	// Create a git repo
+	os.Chdir(tmpDir)
+	exec.Command("git", "init").Run()
+	exec.Command("git", "config", "user.email", "test@test.com").Run()
+	exec.Command("git", "config", "user.name", "Test User").Run()
+
+	// Create initial commit
+	os.WriteFile("test.txt", []byte("test"), 0644)
+	exec.Command("git", "add", "test.txt").Run()
+	exec.Command("git", "commit", "-m", "initial").Run()
+
+	// Should not be in rebase
+	if isInRebase() {
+		t.Error("expected false when not in rebase")
+	}
+}
+
+func TestIsInRebase_InRebase(t *testing.T) {
+	tmpDir := t.TempDir()
+	originalWd, _ := os.Getwd()
+	defer os.Chdir(originalWd)
+
+	// Create a git repo
+	os.Chdir(tmpDir)
+	exec.Command("git", "init").Run()
+	exec.Command("git", "config", "user.email", "test@test.com").Run()
+	exec.Command("git", "config", "user.name", "Test User").Run()
+
+	// Create initial commit
+	os.WriteFile("test.txt", []byte("test"), 0644)
+	exec.Command("git", "add", "test.txt").Run()
+	exec.Command("git", "commit", "-m", "initial").Run()
+
+	// Simulate rebase by creating rebase-merge directory
+	os.MkdirAll(filepath.Join(tmpDir, ".git", "rebase-merge"), 0755)
+
+	// Should detect rebase
+	if !isInRebase() {
+		t.Error("expected true when .git/rebase-merge exists")
+	}
+}
+
+func TestIsInRebase_InRebaseApply(t *testing.T) {
+	tmpDir := t.TempDir()
+	originalWd, _ := os.Getwd()
+	defer os.Chdir(originalWd)
+
+	// Create a git repo
+	os.Chdir(tmpDir)
+	exec.Command("git", "init").Run()
+
+	// Simulate non-interactive rebase by creating rebase-apply directory
+	os.MkdirAll(filepath.Join(tmpDir, ".git", "rebase-apply"), 0755)
+
+	// Should detect rebase
+	if !isInRebase() {
+		t.Error("expected true when .git/rebase-apply exists")
+	}
+}
+
+func TestHasJSONLConflict_NoConflict(t *testing.T) {
+	tmpDir := t.TempDir()
+	originalWd, _ := os.Getwd()
+	defer os.Chdir(originalWd)
+
+	// Create a git repo
+	os.Chdir(tmpDir)
+	exec.Command("git", "init").Run()
+	exec.Command("git", "config", "user.email", "test@test.com").Run()
+	exec.Command("git", "config", "user.name", "Test User").Run()
+
+	// Create initial commit
+	os.WriteFile("test.txt", []byte("test"), 0644)
+	exec.Command("git", "add", "test.txt").Run()
+	exec.Command("git", "commit", "-m", "initial").Run()
+
+	// Should not have JSONL conflict
+	if hasJSONLConflict() {
+		t.Error("expected false when no conflicts")
+	}
+}
+
+func TestHasJSONLConflict_OnlyJSONLConflict(t *testing.T) {
+	tmpDir := t.TempDir()
+	originalWd, _ := os.Getwd()
+	defer os.Chdir(originalWd)
+
+	// Create a git repo
+	os.Chdir(tmpDir)
+	exec.Command("git", "init", "-b", "main").Run()
+	exec.Command("git", "config", "user.email", "test@test.com").Run()
+	exec.Command("git", "config", "user.name", "Test User").Run()
+
+	// Create initial commit
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	os.MkdirAll(beadsDir, 0755)
+	os.WriteFile(filepath.Join(beadsDir, "beads.jsonl"), []byte(`{"id":"bd-1","title":"original"}`), 0644)
+	exec.Command("git", "add", ".").Run()
+	exec.Command("git", "commit", "-m", "initial").Run()
+
+	// Create a second commit on main (modify same issue)
+	os.WriteFile(filepath.Join(beadsDir, "beads.jsonl"), []byte(`{"id":"bd-1","title":"main-version"}`), 0644)
+	exec.Command("git", "add", ".").Run()
+	exec.Command("git", "commit", "-m", "main change").Run()
+
+	// Create a branch from the first commit
+	exec.Command("git", "checkout", "-b", "feature", "HEAD~1").Run()
+	os.WriteFile(filepath.Join(beadsDir, "beads.jsonl"), []byte(`{"id":"bd-1","title":"feature-version"}`), 0644)
+	exec.Command("git", "add", ".").Run()
+	exec.Command("git", "commit", "-m", "feature change").Run()
+
+	// Attempt rebase onto main (will conflict)
+	exec.Command("git", "rebase", "main").Run()
+
+	// Should detect JSONL conflict during rebase
+	if !hasJSONLConflict() {
+		t.Error("expected true when only beads.jsonl has conflict during rebase")
+	}
+}
+
+func TestHasJSONLConflict_MultipleConflicts(t *testing.T) {
+	tmpDir := t.TempDir()
+	originalWd, _ := os.Getwd()
+	defer os.Chdir(originalWd)
+
+	// Create a git repo
+	os.Chdir(tmpDir)
+	exec.Command("git", "init", "-b", "main").Run()
+	exec.Command("git", "config", "user.email", "test@test.com").Run()
+	exec.Command("git", "config", "user.name", "Test User").Run()
+
+	// Create initial commit with beads.jsonl and another file
+	beadsDir := filepath.Join(tmpDir, ".beads")
+	os.MkdirAll(beadsDir, 0755)
+	os.WriteFile(filepath.Join(beadsDir, "beads.jsonl"), []byte(`{"id":"bd-1","title":"original"}`), 0644)
+	os.WriteFile("other.txt", []byte("line1\nline2\nline3"), 0644)
+	exec.Command("git", "add", ".").Run()
+	exec.Command("git", "commit", "-m", "initial").Run()
+
+	// Create a second commit on main (modify both files)
+	os.WriteFile(filepath.Join(beadsDir, "beads.jsonl"), []byte(`{"id":"bd-1","title":"main-version"}`), 0644)
+	os.WriteFile("other.txt", []byte("line1\nmain-version\nline3"), 0644)
+	exec.Command("git", "add", ".").Run()
+	exec.Command("git", "commit", "-m", "main change").Run()
+
+	// Create a branch from the first commit
+	exec.Command("git", "checkout", "-b", "feature", "HEAD~1").Run()
+	os.WriteFile(filepath.Join(beadsDir, "beads.jsonl"), []byte(`{"id":"bd-1","title":"feature-version"}`), 0644)
+	os.WriteFile("other.txt", []byte("line1\nfeature-version\nline3"), 0644)
+	exec.Command("git", "add", ".").Run()
+	exec.Command("git", "commit", "-m", "feature change").Run()
+
+	// Attempt rebase (will conflict on both files)
+	exec.Command("git", "rebase", "main").Run()
+
+	// Should NOT auto-resolve when multiple files conflict
+	if hasJSONLConflict() {
+		t.Error("expected false when multiple files have conflicts (should not auto-resolve)")
+	}
+}