diff --git a/backend/v3/storage/database/database.go b/backend/v3/storage/database/database.go
index 709dda0be0..f11f67a628 100644
--- a/backend/v3/storage/database/database.go
+++ b/backend/v3/storage/database/database.go
@@ -8,6 +8,7 @@ import (
 type Pool interface {
 	Beginner
 	QueryExecutor
+	Migrator
 
 	Acquire(ctx context.Context) (Client, error)
 	Close(ctx context.Context) error
@@ -17,6 +18,7 @@ type Pool interface {
 type Client interface {
 	Beginner
 	QueryExecutor
+	Migrator
 
 	Release(ctx context.Context) error
 }
diff --git a/backend/v3/storage/database/dbmock/database.mock.go b/backend/v3/storage/database/dbmock/database.mock.go
index 215804ded8..02060efb3f 100644
--- a/backend/v3/storage/database/dbmock/database.mock.go
+++ b/backend/v3/storage/database/dbmock/database.mock.go
@@ -199,6 +199,44 @@ func (c *MockPoolExecCall) DoAndReturn(f func(context.Context, string, ...any) e
 	return c
 }
 
+// Migrate mocks base method.
+func (m *MockPool) Migrate(arg0 context.Context) error {
+	m.ctrl.T.Helper()
+	ret := m.ctrl.Call(m, "Migrate", arg0)
+	ret0, _ := ret[0].(error)
+	return ret0
+}
+
+// Migrate indicates an expected call of Migrate.
+func (mr *MockPoolMockRecorder) Migrate(arg0 any) *MockPoolMigrateCall {
+	mr.mock.ctrl.T.Helper()
+	call := mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "Migrate", reflect.TypeOf((*MockPool)(nil).Migrate), arg0)
+	return &MockPoolMigrateCall{Call: call}
+}
+
+// MockPoolMigrateCall wrap *gomock.Call
+type MockPoolMigrateCall struct {
+	*gomock.Call
+}
+
+// Return rewrite *gomock.Call.Return
+func (c *MockPoolMigrateCall) Return(arg0 error) *MockPoolMigrateCall {
+	c.Call = c.Call.Return(arg0)
+	return c
+}
+
+// Do rewrite *gomock.Call.Do
+func (c *MockPoolMigrateCall) Do(f func(context.Context) error) *MockPoolMigrateCall {
+	c.Call = c.Call.Do(f)
+	return c
+}
+
+// DoAndReturn rewrite *gomock.Call.DoAndReturn
+func (c *MockPoolMigrateCall) DoAndReturn(f func(context.Context) error) *MockPoolMigrateCall {
+	c.Call = c.Call.DoAndReturn(f)
+	return c
+}
+
 // Query mocks base method.
 func (m *MockPool) Query(arg0 context.Context, arg1 string, arg2 ...any) (database.Rows, error) {
 	m.ctrl.T.Helper()
@@ -391,6 +429,44 @@ func (c *MockClientExecCall) DoAndReturn(f func(context.Context, string, ...any)
 	return c
 }
 
+// Migrate mocks base method.
+func (m *MockClient) Migrate(arg0 context.Context) error {
+	m.ctrl.T.Helper()
+	ret := m.ctrl.Call(m, "Migrate", arg0)
+	ret0, _ := ret[0].(error)
+	return ret0
+}
+
+// Migrate indicates an expected call of Migrate.
+func (mr *MockClientMockRecorder) Migrate(arg0 any) *MockClientMigrateCall {
+	mr.mock.ctrl.T.Helper()
+	call := mr.mock.ctrl.RecordCallWithMethodType(mr.mock, "Migrate", reflect.TypeOf((*MockClient)(nil).Migrate), arg0)
+	return &MockClientMigrateCall{Call: call}
+}
+
+// MockClientMigrateCall wrap *gomock.Call
+type MockClientMigrateCall struct {
+	*gomock.Call
+}
+
+// Return rewrite *gomock.Call.Return
+func (c *MockClientMigrateCall) Return(arg0 error) *MockClientMigrateCall {
+	c.Call = c.Call.Return(arg0)
+	return c
+}
+
+// Do rewrite *gomock.Call.Do
+func (c *MockClientMigrateCall) Do(f func(context.Context) error) *MockClientMigrateCall {
+	c.Call = c.Call.Do(f)
+	return c
+}
+
+// DoAndReturn rewrite *gomock.Call.DoAndReturn
+func (c *MockClientMigrateCall) DoAndReturn(f func(context.Context) error) *MockClientMigrateCall {
+	c.Call = c.Call.DoAndReturn(f)
+	return c
+}
+
 // Query mocks base method.
 func (m *MockClient) Query(arg0 context.Context, arg1 string, arg2 ...any) (database.Rows, error) {
 	m.ctrl.T.Helper()
diff --git a/backend/v3/storage/database/dialect/postgres/config.go b/backend/v3/storage/database/dialect/postgres/config.go
index 630c603d14..3bab1f8b1f 100644
--- a/backend/v3/storage/database/dialect/postgres/config.go
+++ b/backend/v3/storage/database/dialect/postgres/config.go
@@ -13,8 +13,9 @@ import (
 )
 
 var (
-	_    database.Connector = (*Config)(nil)
-	Name                    = "postgres"
+	_          database.Connector = (*Config)(nil)
+	Name                          = "postgres"
+	isMigrated bool
 )
 
 type Config struct {
@@ -45,7 +46,7 @@ func (c *Config) Connect(ctx context.Context) (database.Pool, error) {
 	if err = pool.Ping(ctx); err != nil {
 		return nil, err
 	}
-	return &pgxPool{pool}, nil
+	return &pgxPool{Pool: pool}, nil
 }
 
 func (c *Config) getPool(ctx context.Context) (*pgxpool.Pool, error) {
diff --git a/backend/v3/storage/database/dialect/postgres/conn.go b/backend/v3/storage/database/dialect/postgres/conn.go
index 5e5942680a..0cb5d8f16a 100644
--- a/backend/v3/storage/database/dialect/postgres/conn.go
+++ b/backend/v3/storage/database/dialect/postgres/conn.go
@@ -9,11 +9,12 @@ import (
 	"github.com/zitadel/zitadel/backend/v3/storage/database/dialect/postgres/migration"
 )
 
-type pgxConn struct{ *pgxpool.Conn }
+type pgxConn struct {
+	*pgxpool.Conn
+}
 
 var (
-	_ database.Client   = (*pgxConn)(nil)
-	_ database.Migrator = (*pgxConn)(nil)
+	_ database.Client = (*pgxConn)(nil)
 )
 
 // Release implements [database.Client].
@@ -53,5 +54,10 @@ func (c *pgxConn) Exec(ctx context.Context, sql string, args ...any) error {
 
 // Migrate implements [database.Migrator].
 func (c *pgxConn) Migrate(ctx context.Context) error {
-	return migration.Migrate(ctx, c.Conn.Conn())
+	if isMigrated {
+		return nil
+	}
+	err := migration.Migrate(ctx, c.Conn.Conn())
+	isMigrated = err == nil
+	return err
 }
diff --git a/backend/v3/storage/database/dialect/postgres/embedded/start.go b/backend/v3/storage/database/dialect/postgres/embedded/start.go
new file mode 100644
index 0000000000..9a5f3ea82b
--- /dev/null
+++ b/backend/v3/storage/database/dialect/postgres/embedded/start.go
@@ -0,0 +1,50 @@
+// embedded is used for testing purposes
+package embedded
+
+import (
+	"net"
+	"os"
+
+	embeddedpostgres "github.com/fergusstrange/embedded-postgres"
+	"github.com/zitadel/logging"
+
+	"github.com/zitadel/zitadel/backend/v3/storage/database"
+	"github.com/zitadel/zitadel/backend/v3/storage/database/dialect/postgres"
+)
+
+// StartEmbedded starts an embedded postgres v16 instance and returns a database connector and a stop function
+// the database is started on a random port and data are stored in a temporary directory
+// its used for testing purposes only
+func StartEmbedded() (connector database.Connector, stop func(), err error) {
+	path, err := os.MkdirTemp("", "zitadel-embedded-postgres-*")
+	logging.OnError(err).Fatal("unable to create temp dir")
+
+	port, close := getPort()
+
+	config := embeddedpostgres.DefaultConfig().Version(embeddedpostgres.V16).Port(uint32(port)).RuntimePath(path)
+	embedded := embeddedpostgres.NewDatabase(config)
+
+	close()
+	err = embedded.Start()
+	logging.OnError(err).Fatal("unable to start db")
+
+	connector, err = postgres.DecodeConfig(config.GetConnectionURL())
+	if err != nil {
+		return nil, nil, err
+	}
+
+	return connector, func() {
+		logging.OnError(embedded.Stop()).Error("unable to stop db")
+	}, nil
+}
+
+// getPort returns a free port and locks it until close is called
+func getPort() (port uint16, close func()) {
+	l, err := net.Listen("tcp", ":0")
+	logging.OnError(err).Fatal("unable to get port")
+	port = uint16(l.Addr().(*net.TCPAddr).Port)
+	logging.WithFields("port", port).Info("Port is available")
+	return port, func() {
+		logging.OnError(l.Close()).Error("unable to close port listener")
+	}
+}
diff --git a/backend/v3/storage/database/dialect/postgres/migration/migrationgs_test.go b/backend/v3/storage/database/dialect/postgres/migration/migrationgs_test.go
new file mode 100644
index 0000000000..37680cb94f
--- /dev/null
+++ b/backend/v3/storage/database/dialect/postgres/migration/migrationgs_test.go
@@ -0,0 +1,60 @@
+package migration_test
+
+import (
+	"context"
+	"testing"
+
+	"github.com/muhlemmer/gu"
+	"github.com/stretchr/testify/assert"
+	"github.com/stretchr/testify/require"
+
+	"github.com/zitadel/zitadel/backend/v3/storage/database"
+	"github.com/zitadel/zitadel/backend/v3/storage/database/dialect/postgres/embedded"
+)
+
+func TestMigrate(t *testing.T) {
+	tests := []struct {
+		name string
+		stmt string
+		args []any
+		res  []any
+	}{
+		{
+			name: "schema",
+			stmt: "SELECT EXISTS(SELECT 1 FROM information_schema.schemata where schema_name = 'zitadel') ;",
+			res:  []any{true},
+		},
+		{
+			name: "001",
+			stmt: "SELECT EXISTS(SELECT 1 FROM pg_catalog.pg_tables WHERE schemaname = 'zitadel' and tablename=$1)",
+			args: []any{"instances"},
+			res:  []any{true},
+		},
+	}
+
+	ctx := context.Background()
+
+	connector, stop, err := embedded.StartEmbedded()
+	require.NoError(t, err, "failed to start embedded postgres")
+	defer stop()
+
+	client, err := connector.Connect(ctx)
+	require.NoError(t, err, "failed to connect to embedded postgres")
+
+	err = client.(database.Migrator).Migrate(ctx)
+	require.NoError(t, err, "failed to execute migration steps")
+
+	for _, tt := range tests {
+		t.Run(tt.name, func(t *testing.T) {
+			got := make([]any, len(tt.res))
+			for i := range got {
+				got[i] = new(any)
+				tt.res[i] = gu.Ptr(tt.res[i])
+			}
+
+			require.NoError(t, client.QueryRow(ctx, tt.stmt, tt.args...).Scan(got...), "failed to execute check query")
+
+			assert.Equal(t, tt.res, got, "query result does not match")
+		})
+	}
+}
diff --git a/backend/v3/storage/database/dialect/postgres/pool.go b/backend/v3/storage/database/dialect/postgres/pool.go
index a8a416f362..e3006d91eb 100644
--- a/backend/v3/storage/database/dialect/postgres/pool.go
+++ b/backend/v3/storage/database/dialect/postgres/pool.go
@@ -9,11 +9,12 @@ import (
 	"github.com/zitadel/zitadel/backend/v3/storage/database/dialect/postgres/migration"
 )
 
-type pgxPool struct{ *pgxpool.Pool }
+type pgxPool struct {
+	*pgxpool.Pool
+}
 
 var (
-	_ database.Pool     = (*pgxPool)(nil)
-	_ database.Migrator = (*pgxPool)(nil)
+	_ database.Pool = (*pgxPool)(nil)
 )
 
 // Acquire implements [database.Pool].
@@ -22,7 +23,7 @@ func (c *pgxPool) Acquire(ctx context.Context) (database.Client, error) {
 	if err != nil {
 		return nil, err
 	}
-	return &pgxConn{conn}, nil
+	return &pgxConn{Conn: conn}, nil
 }
 
 // Query implements [database.Pool].
@@ -62,9 +63,16 @@ func (c *pgxPool) Close(_ context.Context) error {
 
 // Migrate implements [database.Migrator].
 func (c *pgxPool) Migrate(ctx context.Context) error {
+	if isMigrated {
+		return nil
+	}
+
 	client, err := c.Pool.Acquire(ctx)
 	if err != nil {
 		return err
 	}
-	return migration.Migrate(ctx, client.Conn())
+
+	err = migration.Migrate(ctx, client.Conn())
+	isMigrated = err == nil
+	return err
 }
diff --git a/backend/v3/storage/database/migration.go b/backend/v3/storage/database/migration.go
index 7aa1101148..5a5b5af6fc 100644
--- a/backend/v3/storage/database/migration.go
+++ b/backend/v3/storage/database/migration.go
@@ -4,5 +4,6 @@ import "context"
 
 type Migrator interface {
 	// Migrate executes migrations to setup the database.
+	// The method can be called once per running Zitadel.
 	Migrate(ctx context.Context) error
 }
diff --git a/backend/v3/storage/database/repository/org_test.go b/backend/v3/storage/database/repository/org_test.go
new file mode 100644
index 0000000000..996e8d1b2c
--- /dev/null
+++ b/backend/v3/storage/database/repository/org_test.go
@@ -0,0 +1,16 @@
+package repository
+
+import (
+	"context"
+	"testing"
+
+	"github.com/stretchr/testify/assert"
+)
+
+// TestBla is an example and can be removed later
+func TestBla(t *testing.T) {
+	var count int
+	err := pool.QueryRow(context.Background(), "select count(*) from zitadel.instances").Scan(&count)
+	assert.NoError(t, err)
+	assert.Equal(t, 0, count)
+}
diff --git a/backend/v3/storage/database/repository/repository_test.go b/backend/v3/storage/database/repository/repository_test.go
new file mode 100644
index 0000000000..7cbca2114f
--- /dev/null
+++ b/backend/v3/storage/database/repository/repository_test.go
@@ -0,0 +1,41 @@
+package repository
+
+import (
+	"context"
+	"log"
+	"os"
+	"testing"
+
+	"github.com/zitadel/zitadel/backend/v3/storage/database"
+	"github.com/zitadel/zitadel/backend/v3/storage/database/dialect/postgres/embedded"
+)
+
+func TestMain(m *testing.M) {
+	os.Exit(runTests(m))
+}
+
+var pool database.Pool
+
+func runTests(m *testing.M) int {
+	connector, stop, err := embedded.StartEmbedded()
+	if err != nil {
+		log.Fatalf("unable to start embedded postgres: %v", err)
+	}
+	defer stop()
+
+	ctx := context.Background()
+
+	pool, err = connector.Connect(ctx)
+	if err != nil {
+		log.Printf("unable to connect to embedded postgres: %v", err)
+		return 1
+	}
+
+	err = pool.Migrate(ctx)
+	if err != nil {
+		log.Printf("unable to migrate database: %v", err)
+		return 1
+	}
+
+	return m.Run()
+}
diff --git a/cmd/setup/54.go b/cmd/setup/54.go
index a241937261..b31055a9af 100644
--- a/cmd/setup/54.go
+++ b/cmd/setup/54.go
@@ -4,7 +4,6 @@ import (
 	"context"
 	_ "embed"
 
-	v3_db "github.com/zitadel/zitadel/backend/v3/storage/database"
 	"github.com/zitadel/zitadel/backend/v3/storage/database/dialect/postgres"
 	"github.com/zitadel/zitadel/internal/database"
 	"github.com/zitadel/zitadel/internal/eventstore"
@@ -15,18 +14,13 @@ type TransactionalTables struct {
 }
 
 func (mig *TransactionalTables) Execute(ctx context.Context, _ eventstore.Event) error {
-	_, err := mig.dbClient.ExecContext(ctx, "CREATE SCHEMA IF NOT EXISTS zitadel")
-	if err != nil {
-		return err
-	}
-
 	config := &postgres.Config{Pool: mig.dbClient.Pool}
 	pool, err := config.Connect(ctx)
 	if err != nil {
 		return err
 	}
 
-	return pool.(v3_db.Migrator).Migrate(ctx)
+	return pool.Migrate(ctx)
 }
 
 func (mig *TransactionalTables) String() string {