diff --git a/internal/database/database.go b/internal/database/database.go
index ddc01ed..b724b89 100644
--- a/internal/database/database.go
+++ b/internal/database/database.go
@@ -21,6 +21,10 @@ import (
 //go:embed schema/*.sql
 var schemaFS embed.FS
 
+// bootstrapVersion is the migration that creates the schema_migrations
+// table itself. It is applied before the normal migration loop.
+const bootstrapVersion = "000"
+
 // Params defines dependencies for Database.
 type Params struct {
 	fx.In
@@ -143,17 +147,86 @@ func collectMigrations() ([]string, error) {
 	return migrations, nil
 }
 
-// ensureMigrationsTable creates the schema_migrations tracking table if
-// it does not already exist.
-func ensureMigrationsTable(ctx context.Context, db *sql.DB) error {
-	_, err := db.ExecContext(ctx, `
-		CREATE TABLE IF NOT EXISTS schema_migrations (
-			version TEXT PRIMARY KEY,
-			applied_at DATETIME DEFAULT CURRENT_TIMESTAMP
-		)
-	`)
+// bootstrapMigrationsTable ensures the schema_migrations table exists
+// by applying 000.sql directly. For databases that already have the
+// table (created by older code), it records version "000" for
+// consistency.
+func bootstrapMigrationsTable(ctx context.Context, db *sql.DB, log *slog.Logger) error {
+	var tableExists int
+
+	err := db.QueryRowContext(ctx,
+		"SELECT COUNT(*) FROM sqlite_master WHERE type='table' AND name='schema_migrations'",
+	).Scan(&tableExists)
 	if err != nil {
-		return fmt.Errorf("failed to create migrations table: %w", err)
+		return fmt.Errorf("failed to check for migrations table: %w", err)
+	}
+
+	if tableExists > 0 {
+		return ensureBootstrapVersionRecorded(ctx, db, log)
+	}
+
+	return applyBootstrapMigration(ctx, db, log)
+}
+
+// ensureBootstrapVersionRecorded checks whether version "000" is already
+// recorded in an existing schema_migrations table and inserts it if not.
+func ensureBootstrapVersionRecorded(ctx context.Context, db *sql.DB, log *slog.Logger) error {
+	var recorded int
+
+	err := db.QueryRowContext(ctx,
+		"SELECT COUNT(*) FROM schema_migrations WHERE version = ?",
+		bootstrapVersion,
+	).Scan(&recorded)
+	if err != nil {
+		return fmt.Errorf("failed to check bootstrap migration status: %w", err)
+	}
+
+	if recorded > 0 {
+		return nil
+	}
+
+	_, err = db.ExecContext(ctx,
+		"INSERT INTO schema_migrations (version) VALUES (?)",
+		bootstrapVersion,
+	)
+	if err != nil {
+		return fmt.Errorf("failed to record bootstrap migration: %w", err)
+	}
+
+	if log != nil {
+		log.Info("recorded bootstrap migration for existing table", "version", bootstrapVersion)
+	}
+
+	return nil
+}
+
+// applyBootstrapMigration reads and executes 000.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 := schemaFS.ReadFile("schema/000.sql")
+	if err != nil {
+		return fmt.Errorf("failed to read bootstrap migration 000.sql: %w", err)
+	}
+
+	if log != nil {
+		log.Info("applying bootstrap migration", "version", bootstrapVersion)
+	}
+
+	_, err = db.ExecContext(ctx, string(content))
+	if err != nil {
+		return fmt.Errorf("failed to apply bootstrap migration: %w", err)
+	}
+
+	_, err = db.ExecContext(ctx,
+		"INSERT INTO schema_migrations (version) VALUES (?)",
+		bootstrapVersion,
+	)
+	if err != nil {
+		return fmt.Errorf("failed to record bootstrap migration: %w", err)
+	}
+
+	if log != nil {
+		log.Info("bootstrap migration applied successfully", "version", bootstrapVersion)
 	}
 
 	return nil
@@ -164,7 +237,7 @@ func ensureMigrationsTable(ctx context.Context, db *sql.DB) error {
 // This is exported so tests can apply the real schema without the full fx
 // lifecycle.
 func ApplyMigrations(ctx context.Context, db *sql.DB, log *slog.Logger) error {
-	if err := ensureMigrationsTable(ctx, db); err != nil {
+	if err := bootstrapMigrationsTable(ctx, db, log); err != nil {
 		return err
 	}
 
diff --git a/internal/database/database_test.go b/internal/database/database_test.go
index 9c2fc2c..ede0d1c 100644
--- a/internal/database/database_test.go
+++ b/internal/database/database_test.go
@@ -8,6 +8,20 @@ import (
 	_ "modernc.org/sqlite" // SQLite driver registration
 )
 
+// openTestDB returns a fresh in-memory SQLite database.
+func openTestDB(t *testing.T) *sql.DB {
+	t.Helper()
+
+	db, err := sql.Open("sqlite", ":memory:")
+	if err != nil {
+		t.Fatalf("failed to open test db: %v", err)
+	}
+
+	t.Cleanup(func() { db.Close() })
+
+	return db
+}
+
 func TestParseMigrationVersion(t *testing.T) {
 	tests := []struct {
 		name     string
@@ -86,70 +100,180 @@ func TestParseMigrationVersion(t *testing.T) {
 	}
 }
 
-func TestApplyMigrations(t *testing.T) {
-	db, err := sql.Open("sqlite", ":memory:")
-	if err != nil {
-		t.Fatalf("failed to open in-memory database: %v", err)
-	}
-	defer db.Close()
+func TestApplyMigrations_CreatesSchemaAndTables(t *testing.T) {
+	db := openTestDB(t)
+	ctx := context.Background()
 
-	// Apply migrations should succeed.
-	if err := ApplyMigrations(context.Background(), db, nil); err != nil {
+	if err := ApplyMigrations(ctx, db, nil); err != nil {
 		t.Fatalf("ApplyMigrations failed: %v", err)
 	}
 
-	// Verify the schema_migrations table recorded the version.
-	var version string
-
-	err = db.QueryRowContext(context.Background(),
-		"SELECT version FROM schema_migrations LIMIT 1",
-	).Scan(&version)
+	// The schema_migrations table must exist and contain at least
+	// version "000" (the bootstrap) and "001" (the initial schema).
+	rows, err := db.Query("SELECT version FROM schema_migrations ORDER BY version")
 	if err != nil {
 		t.Fatalf("failed to query schema_migrations: %v", err)
 	}
+	defer rows.Close()
 
-	if version != "001" {
-		t.Errorf("expected version %q, got %q", "001", version)
+	var versions []string
+	for rows.Next() {
+		var v string
+		if err := rows.Scan(&v); err != nil {
+			t.Fatalf("failed to scan version: %v", err)
+		}
+
+		versions = append(versions, v)
 	}
 
-	// Verify a table from the migration exists (source_content).
-	var tableName string
+	if err := rows.Err(); err != nil {
+		t.Fatalf("row iteration error: %v", err)
+	}
 
-	err = db.QueryRowContext(context.Background(),
-		"SELECT name FROM sqlite_master WHERE type='table' AND name='source_content'",
-	).Scan(&tableName)
-	if err != nil {
-		t.Fatalf("expected source_content table to exist: %v", err)
+	if len(versions) < 2 {
+		t.Fatalf("expected at least 2 migrations recorded, got %d: %v", len(versions), versions)
+	}
+
+	if versions[0] != "000" {
+		t.Errorf("first recorded migration = %q, want %q", versions[0], "000")
+	}
+
+	if versions[1] != "001" {
+		t.Errorf("second recorded migration = %q, want %q", versions[1], "001")
+	}
+
+	// Verify that the application tables created by 001.sql exist.
+	for _, table := range []string{"source_content", "source_metadata", "output_content", "request_cache", "negative_cache", "cache_stats"} {
+		var count int
+
+		err := db.QueryRow(
+			"SELECT COUNT(*) FROM sqlite_master WHERE type='table' AND name=?",
+			table,
+		).Scan(&count)
+		if err != nil {
+			t.Fatalf("failed to check for table %s: %v", table, err)
+		}
+
+		if count != 1 {
+			t.Errorf("table %s does not exist after migrations", table)
+		}
 	}
 }
 
-func TestApplyMigrationsIdempotent(t *testing.T) {
-	db, err := sql.Open("sqlite", ":memory:")
-	if err != nil {
-		t.Fatalf("failed to open in-memory database: %v", err)
-	}
-	defer db.Close()
+func TestApplyMigrations_Idempotent(t *testing.T) {
+	db := openTestDB(t)
+	ctx := context.Background()
 
-	// Apply twice should succeed (idempotent).
-	if err := ApplyMigrations(context.Background(), db, nil); err != nil {
+	if err := ApplyMigrations(ctx, db, nil); err != nil {
 		t.Fatalf("first ApplyMigrations failed: %v", err)
 	}
 
-	if err := ApplyMigrations(context.Background(), db, nil); err != nil {
+	// Running a second time must succeed without errors.
+	if err := ApplyMigrations(ctx, db, nil); err != nil {
 		t.Fatalf("second ApplyMigrations failed: %v", err)
 	}
 
-	// Should still have exactly one migration recorded.
+	// Verify no duplicate rows in schema_migrations.
 	var count int
 
-	err = db.QueryRowContext(context.Background(),
-		"SELECT COUNT(*) FROM schema_migrations",
-	).Scan(&count)
+	err := db.QueryRow("SELECT COUNT(*) FROM schema_migrations WHERE version = '000'").Scan(&count)
 	if err != nil {
-		t.Fatalf("failed to count schema_migrations: %v", err)
+		t.Fatalf("failed to count 000 rows: %v", err)
 	}
 
 	if count != 1 {
-		t.Errorf("expected 1 migration record, got %d", count)
+		t.Errorf("expected exactly 1 row for version 000, got %d", count)
+	}
+}
+
+func TestBootstrapMigrationsTable_FreshDatabase(t *testing.T) {
+	db := openTestDB(t)
+	ctx := context.Background()
+
+	if err := bootstrapMigrationsTable(ctx, db, nil); err != nil {
+		t.Fatalf("bootstrapMigrationsTable failed: %v", err)
+	}
+
+	// schema_migrations table must exist.
+	var tableCount int
+
+	err := db.QueryRow(
+		"SELECT COUNT(*) FROM sqlite_master WHERE type='table' AND name='schema_migrations'",
+	).Scan(&tableCount)
+	if err != nil {
+		t.Fatalf("failed to check for table: %v", err)
+	}
+
+	if tableCount != 1 {
+		t.Fatalf("schema_migrations table not created")
+	}
+
+	// Version "000" must be recorded.
+	var recorded int
+
+	err = db.QueryRow(
+		"SELECT COUNT(*) FROM schema_migrations WHERE version = '000'",
+	).Scan(&recorded)
+	if err != nil {
+		t.Fatalf("failed to check version: %v", err)
+	}
+
+	if recorded != 1 {
+		t.Errorf("expected version 000 to be recorded, got count %d", recorded)
+	}
+}
+
+func TestBootstrapMigrationsTable_ExistingTableBackwardsCompat(t *testing.T) {
+	db := openTestDB(t)
+	ctx := context.Background()
+
+	// Simulate an older database that created the table via inline SQL
+	// (without recording version "000").
+	_, err := db.Exec(`
+		CREATE TABLE schema_migrations (
+			version TEXT PRIMARY KEY,
+			applied_at DATETIME DEFAULT CURRENT_TIMESTAMP
+		)
+	`)
+	if err != nil {
+		t.Fatalf("failed to create legacy table: %v", err)
+	}
+
+	// Insert a fake migration to prove the table already existed.
+	_, err = db.Exec("INSERT INTO schema_migrations (version) VALUES ('001')")
+	if err != nil {
+		t.Fatalf("failed to insert legacy version: %v", err)
+	}
+
+	if err := bootstrapMigrationsTable(ctx, db, nil); err != nil {
+		t.Fatalf("bootstrapMigrationsTable failed: %v", err)
+	}
+
+	// Version "000" must now be recorded.
+	var recorded int
+
+	err = db.QueryRow(
+		"SELECT COUNT(*) FROM schema_migrations WHERE version = '000'",
+	).Scan(&recorded)
+	if err != nil {
+		t.Fatalf("failed to check version: %v", err)
+	}
+
+	if recorded != 1 {
+		t.Errorf("expected version 000 to be recorded for legacy DB, got count %d", recorded)
+	}
+
+	// The existing "001" row must still be there.
+	var legacyCount int
+
+	err = db.QueryRow(
+		"SELECT COUNT(*) FROM schema_migrations WHERE version = '001'",
+	).Scan(&legacyCount)
+	if err != nil {
+		t.Fatalf("failed to check legacy version: %v", err)
+	}
+
+	if legacyCount != 1 {
+		t.Errorf("legacy version 001 row missing after bootstrap")
 	}
 }
diff --git a/internal/database/schema/000.sql b/internal/database/schema/000.sql
new file mode 100644
index 0000000..c05b915
--- /dev/null
+++ b/internal/database/schema/000.sql
@@ -0,0 +1,9 @@
+-- Migration 000: Schema migrations tracking table
+-- This must be the first migration applied. The bootstrap logic in
+-- database.go applies it directly (bypassing the normal migration
+-- loop) when the schema_migrations table does not yet exist.
+
+CREATE TABLE IF NOT EXISTS schema_migrations (
+    version TEXT PRIMARY KEY,
+    applied_at DATETIME DEFAULT CURRENT_TIMESTAMP
+);