diff --git a/internal/storage/sqlite/migrations/002_external_ref_column.go b/internal/storage/sqlite/migrations/002_external_ref_column.go
index e5d2f0c4..fea879e6 100644
--- a/internal/storage/sqlite/migrations/002_external_ref_column.go
+++ b/internal/storage/sqlite/migrations/002_external_ref_column.go
@@ -39,5 +39,11 @@ func MigrateExternalRefColumn(db *sql.DB) error {
 		}
 	}
 
+	// Create index on external_ref (idempotent)
+	_, err = db.Exec(`CREATE INDEX IF NOT EXISTS idx_issues_external_ref ON issues(external_ref)`)
+	if err != nil {
+		return fmt.Errorf("failed to create index on external_ref: %w", err)
+	}
+
 	return nil
 }
diff --git a/internal/storage/sqlite/schema.go b/internal/storage/sqlite/schema.go
index e54b5894..65f68cfe 100644
--- a/internal/storage/sqlite/schema.go
+++ b/internal/storage/sqlite/schema.go
@@ -30,7 +30,7 @@ CREATE INDEX IF NOT EXISTS idx_issues_status ON issues(status);
 CREATE INDEX IF NOT EXISTS idx_issues_priority ON issues(priority);
 CREATE INDEX IF NOT EXISTS idx_issues_assignee ON issues(assignee);
 CREATE INDEX IF NOT EXISTS idx_issues_created_at ON issues(created_at);
-CREATE INDEX IF NOT EXISTS idx_issues_external_ref ON issues(external_ref);
+-- Note: idx_issues_external_ref is created in migrations/002_external_ref_column.go
 
 -- Dependencies table
 CREATE TABLE IF NOT EXISTS dependencies (