diff --git a/internal/database/migrations.go b/internal/database/migrations.go
index 4636340..4ab4996 100644
--- a/internal/database/migrations.go
+++ b/internal/database/migrations.go
@@ -83,8 +83,9 @@ func collectMigrations() ([]string, error) {
 }
 
 // bootstrapMigrationsTable ensures the schema_migrations table exists by
-// applying 000.sql if the table is missing. For databases with a legacy
-// TEXT-based schema_migrations table, it converts to the new INTEGER format.
+// applying 000_migration.sql if the table is missing. For databases with a
+// legacy TEXT-based schema_migrations table, it converts to the new INTEGER
+// format.
 func bootstrapMigrationsTable(ctx context.Context, db *sql.DB, log *slog.Logger) error {
 	var tableExists int
 
@@ -103,12 +104,12 @@ func bootstrapMigrationsTable(ctx context.Context, db *sql.DB, log *slog.Logger)
 	return convertLegacyMigrations(ctx, db, log)
 }
 
-// applyBootstrapMigration reads and executes 000.sql to create the
+// applyBootstrapMigration reads and executes 000_migration.sql to create the
 // schema_migrations table on a fresh database.
 func applyBootstrapMigration(ctx context.Context, db *sql.DB, log *slog.Logger) error {
-	content, err := migrationsFS.ReadFile("migrations/000.sql")
+	content, err := migrationsFS.ReadFile("migrations/000_migration.sql")
 	if err != nil {
-		return fmt.Errorf("failed to read bootstrap migration 000.sql: %w", err)
+		return fmt.Errorf("failed to read bootstrap migration 000_migration.sql: %w", err)
 	}
 
 	if log != nil {
@@ -211,31 +212,48 @@ func readLegacyVersions(ctx context.Context, db *sql.DB) ([]int, error) {
 }
 
 // rebuildMigrationsTable drops the old schema_migrations table, recreates it
-// via 000.sql, and re-inserts the given integer versions.
+// via 000_migration.sql, and re-inserts the given integer versions. The entire
+// operation runs in a single transaction so a crash cannot lose migration data.
 func rebuildMigrationsTable(ctx context.Context, db *sql.DB, versions []int) error {
-	_, err := db.ExecContext(ctx, "DROP TABLE schema_migrations")
+	content, err := migrationsFS.ReadFile("migrations/000_migration.sql")
+	if err != nil {
+		return fmt.Errorf("failed to read bootstrap migration 000_migration.sql: %w", err)
+	}
+
+	tx, err := db.BeginTx(ctx, nil)
+	if err != nil {
+		return fmt.Errorf("failed to begin transaction for legacy conversion: %w", err)
+	}
+
+	defer func() {
+		if err != nil {
+			_ = tx.Rollback()
+		}
+	}()
+
+	_, err = tx.ExecContext(ctx, "DROP TABLE schema_migrations")
 	if err != nil {
 		return fmt.Errorf("failed to drop legacy migrations table: %w", err)
 	}
 
-	content, err := migrationsFS.ReadFile("migrations/000.sql")
-	if err != nil {
-		return fmt.Errorf("failed to read bootstrap migration 000.sql: %w", err)
-	}
-
-	_, err = db.ExecContext(ctx, string(content))
+	_, err = tx.ExecContext(ctx, string(content))
 	if err != nil {
 		return fmt.Errorf("failed to create new migrations table: %w", err)
 	}
 
 	for _, v := range versions {
-		_, insErr := db.ExecContext(ctx,
+		_, err = tx.ExecContext(ctx,
 			"INSERT OR IGNORE INTO schema_migrations (version) VALUES (?)", v)
-		if insErr != nil {
-			return fmt.Errorf("failed to insert converted version %d: %w", v, insErr)
+		if err != nil {
+			return fmt.Errorf("failed to insert converted version %d: %w", v, err)
 		}
 	}
 
+	err = tx.Commit()
+	if err != nil {
+		return fmt.Errorf("failed to commit legacy conversion: %w", err)
+	}
+
 	return nil
 }
 
diff --git a/internal/database/migrations/000.sql b/internal/database/migrations/000_migration.sql
similarity index 100%
rename from internal/database/migrations/000.sql
rename to internal/database/migrations/000_migration.sql
diff --git a/internal/database/migrations_test.go b/internal/database/migrations_test.go
index 12f0f64..fe6bc47 100644
--- a/internal/database/migrations_test.go
+++ b/internal/database/migrations_test.go
@@ -20,7 +20,7 @@ func TestParseMigrationVersion(t *testing.T) {
 		wantVersion int
 		wantErr     bool
 	}{
-		{filename: "000.sql", wantVersion: 0},
+		{filename: "000_migration.sql", wantVersion: 0},
 		{filename: "001_initial.sql", wantVersion: 1},
 		{filename: "002_remove_container_id.sql", wantVersion: 2},
 		{filename: "007_add_resource_limits.sql", wantVersion: 7},