diff --git a/cmd/server/main.go b/cmd/server/main.go
index 040930e..2291ca1 100644
--- a/cmd/server/main.go
+++ b/cmd/server/main.go
@@ -4,6 +4,7 @@ import (
 	"log"
 	"net/http"
 	"os"
+	"regexp"
 	"strings"
 
 	"github.com/gorilla/mux"
@@ -248,6 +249,11 @@ func main() {
 func runMigrations(db *database.DB) error {
 	log.Println("Running database migrations...")
 
+	// Compile regex pattern once for efficiency
+	// Only process numbered migrations (e.g., 001_init.sql, 002_sample_data.sql)
+	// Skip helper scripts like bootstrap_existing_db.sql
+	migrationPattern := regexp.MustCompile(`^\d{3}_.*\.sql$`)
+
 	// Create migrations tracking table if it doesn't exist
 	createTableSQL := `
 		CREATE TABLE IF NOT EXISTS schema_migrations (
@@ -289,6 +295,12 @@ func runMigrations(db *database.DB) error {
 			continue
 		}
 
+		// Skip non-numbered migration files (e.g., bootstrap scripts)
+		if !migrationPattern.MatchString(entry.Name()) {
+			log.Printf("Skipping non-numbered migration file: %s", entry.Name())
+			continue
+		}
+
 		// Skip if already applied
 		if appliedMigrations[entry.Name()] {
 			continue