diff --git a/cmd/bd/daemon_sync.go b/cmd/bd/daemon_sync.go
index ee0318b9..df2f8e31 100644
--- a/cmd/bd/daemon_sync.go
+++ b/cmd/bd/daemon_sync.go
@@ -12,11 +12,28 @@ import (
 
 	"github.com/steveyegge/beads"
 	"github.com/steveyegge/beads/internal/storage"
+	"github.com/steveyegge/beads/internal/storage/sqlite"
 	"github.com/steveyegge/beads/internal/types"
 )
 
-// exportToJSONLWithStore exports issues to JSONL using the provided store
+// exportToJSONLWithStore exports issues to JSONL using the provided store.
+// If multi-repo mode is configured, routes issues to their respective JSONL files.
+// Otherwise, exports to a single JSONL file.
 func exportToJSONLWithStore(ctx context.Context, store storage.Storage, jsonlPath string) error {
+	// Try multi-repo export first
+	sqliteStore, ok := store.(*sqlite.SQLiteStorage)
+	if ok {
+		results, err := sqliteStore.ExportToMultiRepo(ctx)
+		if err != nil {
+			return fmt.Errorf("multi-repo export failed: %w", err)
+		}
+		if results != nil {
+			// Multi-repo mode active - export succeeded
+			return nil
+		}
+	}
+
+	// Single-repo mode - use existing logic
 	// Get all issues
 	issues, err := store.SearchIssues(ctx, "", types.IssueFilter{})
 	if err != nil {
@@ -120,6 +137,20 @@ func exportToJSONLWithStore(ctx context.Context, store storage.Storage, jsonlPat
 
 // importToJSONLWithStore imports issues from JSONL using the provided store
 func importToJSONLWithStore(ctx context.Context, store storage.Storage, jsonlPath string) error {
+	// Try multi-repo import first
+	sqliteStore, ok := store.(*sqlite.SQLiteStorage)
+	if ok {
+		results, err := sqliteStore.HydrateFromMultiRepo(ctx)
+		if err != nil {
+			return fmt.Errorf("multi-repo import failed: %w", err)
+		}
+		if results != nil {
+			// Multi-repo mode active - import succeeded
+			return nil
+		}
+	}
+
+	// Single-repo mode - use existing logic
 	// Read JSONL file
 	file, err := os.Open(jsonlPath) // #nosec G304 - controlled path from config
 	if err != nil {
diff --git a/cmd/bd/repo.go b/cmd/bd/repo.go
new file mode 100644
index 00000000..3236cea9
--- /dev/null
+++ b/cmd/bd/repo.go
@@ -0,0 +1,228 @@
+package main
+
+import (
+	"context"
+	"encoding/json"
+	"fmt"
+	"os"
+	"strings"
+
+	"github.com/spf13/cobra"
+	"github.com/steveyegge/beads/internal/storage"
+)
+
+var repoCmd = &cobra.Command{
+	Use:   "repo",
+	Short: "Manage multiple repository configuration",
+	Long: `Configure and manage multiple repository support for multi-clone sync.
+
+Examples:
+  bd repo add ~/.beads-planning      # Add planning repo
+  bd repo add ../other-repo "notes"  # Add with alias
+  bd repo list                       # Show all configured repos
+  bd repo remove notes               # Remove by alias
+  bd repo remove ~/.beads-planning   # Remove by path`,
+}
+
+var repoAddCmd = &cobra.Command{
+	Use:   "add <path> [alias]",
+	Short: "Add an additional repository to sync",
+	Args:  cobra.RangeArgs(1, 2),
+	RunE: func(cmd *cobra.Command, args []string) error {
+		if err := ensureDirectMode("repo add requires direct database access"); err != nil {
+			return err
+		}
+
+		ctx := context.Background()
+		path := args[0]
+		var alias string
+		if len(args) > 1 {
+			alias = args[1]
+		}
+
+		// Use path as key if no alias provided
+		key := alias
+		if key == "" {
+			key = path
+		}
+
+		// Get existing repos
+		existing, err := getRepoConfig(ctx, store)
+		if err != nil {
+			return fmt.Errorf("failed to get existing repos: %w", err)
+		}
+
+		existing[key] = path
+
+		// Save back
+		if err := setRepoConfig(ctx, store, existing); err != nil {
+			return fmt.Errorf("failed to save config: %w", err)
+		}
+
+		if jsonOutput {
+			result := map[string]interface{}{
+				"added": true,
+				"key":   key,
+				"path":  path,
+			}
+			return json.NewEncoder(os.Stdout).Encode(result)
+		}
+
+		fmt.Printf("Added repository: %s → %s\n", key, path)
+		return nil
+	},
+}
+
+var repoRemoveCmd = &cobra.Command{
+	Use:   "remove <key>",
+	Short: "Remove a repository from sync configuration",
+	Args:  cobra.ExactArgs(1),
+	RunE: func(cmd *cobra.Command, args []string) error {
+		if err := ensureDirectMode("repo remove requires direct database access"); err != nil {
+			return err
+		}
+
+		ctx := context.Background()
+		key := args[0]
+
+		// Get existing repos
+		existing, err := getRepoConfig(ctx, store)
+		if err != nil {
+			return fmt.Errorf("failed to get existing repos: %w", err)
+		}
+
+		path, exists := existing[key]
+		if !exists {
+			return fmt.Errorf("repository not found: %s", key)
+		}
+
+		delete(existing, key)
+
+		// Save back
+		if err := setRepoConfig(ctx, store, existing); err != nil {
+			return fmt.Errorf("failed to save config: %w", err)
+		}
+
+		if jsonOutput {
+			result := map[string]interface{}{
+				"removed": true,
+				"key":     key,
+				"path":    path,
+			}
+			return json.NewEncoder(os.Stdout).Encode(result)
+		}
+
+		fmt.Printf("Removed repository: %s → %s\n", key, path)
+		return nil
+	},
+}
+
+var repoListCmd = &cobra.Command{
+	Use:   "list",
+	Short: "List all configured repositories",
+	RunE: func(cmd *cobra.Command, args []string) error {
+		if err := ensureDirectMode("repo list requires direct database access"); err != nil {
+			return err
+		}
+
+		ctx := context.Background()
+		repos, err := getRepoConfig(ctx, store)
+		if err != nil {
+			return fmt.Errorf("failed to load config: %w", err)
+		}
+
+		if jsonOutput {
+			result := map[string]interface{}{
+				"primary":    ".",
+				"additional": repos,
+			}
+			return json.NewEncoder(os.Stdout).Encode(result)
+		}
+
+		fmt.Println("Primary repository: .")
+		if len(repos) == 0 {
+			fmt.Println("No additional repositories configured")
+		} else {
+			fmt.Println("\nAdditional repositories:")
+			for key, path := range repos {
+				fmt.Printf("  %s → %s\n", key, path)
+			}
+		}
+		return nil
+	},
+}
+
+var repoSyncCmd = &cobra.Command{
+	Use:   "sync",
+	Short: "Manually trigger multi-repo sync",
+	RunE: func(cmd *cobra.Command, args []string) error {
+		if err := ensureDirectMode("repo sync requires direct database access"); err != nil {
+			return err
+		}
+
+		ctx := context.Background()
+
+		// Import from all repos
+		jsonlPath := findJSONLPath()
+		if err := importToJSONLWithStore(ctx, store, jsonlPath); err != nil {
+			return fmt.Errorf("import failed: %w", err)
+		}
+
+		// Export to all repos
+		if err := exportToJSONLWithStore(ctx, store, jsonlPath); err != nil {
+			return fmt.Errorf("export failed: %w", err)
+		}
+
+		if jsonOutput {
+			result := map[string]interface{}{
+				"synced": true,
+			}
+			return json.NewEncoder(os.Stdout).Encode(result)
+		}
+
+		fmt.Println("Multi-repo sync complete")
+		return nil
+	},
+}
+
+// Helper functions for repo config management
+func getRepoConfig(ctx context.Context, store storage.Storage) (map[string]string, error) {
+	value, err := store.GetConfig(ctx, "repos.additional")
+	if err != nil {
+		if strings.Contains(err.Error(), "not found") {
+			return make(map[string]string), nil
+		}
+		return nil, err
+	}
+
+	// Parse JSON map
+	repos := make(map[string]string)
+	if err := json.Unmarshal([]byte(value), &repos); err != nil {
+		return nil, fmt.Errorf("failed to parse repos config: %w", err)
+	}
+
+	return repos, nil
+}
+
+func setRepoConfig(ctx context.Context, store storage.Storage, repos map[string]string) error {
+	data, err := json.Marshal(repos)
+	if err != nil {
+		return fmt.Errorf("failed to serialize repos: %w", err)
+	}
+
+	return store.SetConfig(ctx, "repos.additional", string(data))
+}
+
+func init() {
+	repoCmd.AddCommand(repoAddCmd)
+	repoCmd.AddCommand(repoRemoveCmd)
+	repoCmd.AddCommand(repoListCmd)
+	repoCmd.AddCommand(repoSyncCmd)
+
+	repoAddCmd.Flags().BoolVar(&jsonOutput, "json", false, "Output JSON")
+	repoRemoveCmd.Flags().BoolVar(&jsonOutput, "json", false, "Output JSON")
+	repoListCmd.Flags().BoolVar(&jsonOutput, "json", false, "Output JSON")
+	repoSyncCmd.Flags().BoolVar(&jsonOutput, "json", false, "Output JSON")
+
+	rootCmd.AddCommand(repoCmd)
+}