diff --git a/roomserver/storage/postgres/storage.go b/roomserver/storage/postgres/storage.go
index f47a64c80..413163704 100644
--- a/roomserver/storage/postgres/storage.go
+++ b/roomserver/storage/postgres/storage.go
@@ -16,10 +16,13 @@
 package postgres
 
 import (
+	"context"
 	"database/sql"
 	"fmt"
 
 	"github.com/lib/pq"
+	"github.com/sirupsen/logrus"
+
 	// Import the postgres database driver.
 	_ "github.com/lib/pq"
 
@@ -52,30 +55,8 @@ func Open(base *base.BaseDendrite, dbProperties *config.DatabaseOptions, cache c
 
 	// Special case, since this migration uses several tables, so it needs to
 	// be sure that all tables are created first.
-	// TODO: Remove when we are sure we are not having goose artefacts in the db
-	// This forces an error, which indicates the migration is already applied, since the
-	// column event_nid was removed from the table
-	var eventNID int
-	err = db.QueryRow("SELECT event_nid FROM roomserver_state_block LIMIT 1;").Scan(&eventNID)
-	if err == nil {
-		m := sqlutil.NewMigrator(db)
-		m.AddMigrations(sqlutil.Migration{
-			Version: "roomserver: state blocks refactor",
-			Up:      deltas.UpStateBlocksRefactor,
-		})
-		if err = m.Up(base.Context()); err != nil {
-			return nil, err
-		}
-	} else {
-		switch e := err.(type) {
-		case *pq.Error:
-			// ignore undefined_column (42703) errors, as this is expected at this point
-			if e.Code != "42703" {
-				return nil, err
-			}
-		default:
-			return nil, err
-		}
+	if err = executeMigration(base.Context(), db); err != nil {
+		return nil, err
 	}
 
 	// Then prepare the statements. Now that the migrations have run, any columns referred
@@ -87,6 +68,50 @@ func Open(base *base.BaseDendrite, dbProperties *config.DatabaseOptions, cache c
 	return &d, nil
 }
 
+func executeMigration(ctx context.Context, db *sql.DB) error {
+	// TODO: Remove when we are sure we are not having goose artefacts in the db
+	// This forces an error, which indicates the migration is already applied, since the
+	// column event_nid was removed from the table
+	migrationName := "roomserver: state blocks refactor"
+	var migrationCount int
+
+	err := db.QueryRowContext(ctx, "SELECT count(*) FROM db_migrations WHERE version = $1", migrationName).Scan(&migrationCount)
+	if err != nil {
+		return err
+	}
+	if migrationCount > 0 {
+		return nil
+	}
+
+	var eventNID int
+	err = db.QueryRowContext(ctx, "SELECT event_nid FROM roomserver_state_block LIMIT 1;").Scan(&eventNID)
+	if err == nil {
+		m := sqlutil.NewMigrator(db)
+		m.AddMigrations(sqlutil.Migration{
+			Version: migrationName,
+			Up:      deltas.UpStateBlocksRefactor,
+		})
+		if err = m.Up(ctx); err != nil {
+			return err
+		}
+	} else {
+		switch e := err.(type) {
+		case *pq.Error:
+			// ignore undefined_column (42703) errors, as this is expected at this point
+			if e.Code != "42703" {
+				return err
+			}
+			if err = sqlutil.InsertMigration(ctx, db, migrationName); err != nil {
+				// not a fatal error, log and continue
+				logrus.WithError(err).Warnf("unable to manually insert migration '%s'", migrationName)
+			}
+		default:
+			return err
+		}
+	}
+	return nil
+}
+
 func (d *Database) create(db *sql.DB) error {
 	if err := CreateEventStateKeysTable(db); err != nil {
 		return err
diff --git a/roomserver/storage/sqlite3/storage.go b/roomserver/storage/sqlite3/storage.go
index 9f8a1b118..3c7996d85 100644
--- a/roomserver/storage/sqlite3/storage.go
+++ b/roomserver/storage/sqlite3/storage.go
@@ -19,8 +19,11 @@ import (
 	"context"
 	"database/sql"
 	"fmt"
+	"strings"
 
 	"github.com/matrix-org/gomatrixserverlib"
+	"github.com/mattn/go-sqlite3"
+	"github.com/sirupsen/logrus"
 
 	"github.com/matrix-org/dendrite/internal/caching"
 	"github.com/matrix-org/dendrite/internal/sqlutil"
@@ -61,20 +64,8 @@ func Open(base *base.BaseDendrite, dbProperties *config.DatabaseOptions, cache c
 
 	// Special case, since this migration uses several tables, so it needs to
 	// be sure that all tables are created first.
-	// TODO: Remove when we are sure we are not having goose artefacts in the db
-	// This forces an error, which indicates the migration is already applied, since the
-	// column event_nid was removed from the table
-	var eventNID int
-	err = db.QueryRow("SELECT event_nid FROM roomserver_state_block LIMIT 1;").Scan(&eventNID)
-	if err == nil {
-		m := sqlutil.NewMigrator(db)
-		m.AddMigrations(sqlutil.Migration{
-			Version: "roomserver: state blocks refactor",
-			Up:      deltas.UpStateBlocksRefactor,
-		})
-		if err = m.Up(base.Context()); err != nil {
-			return nil, err
-		}
+	if err = executeMigration(base.Context(), db); err != nil {
+		return nil, err
 	}
 
 	// Then prepare the statements. Now that the migrations have run, any columns referred
@@ -86,6 +77,52 @@ func Open(base *base.BaseDendrite, dbProperties *config.DatabaseOptions, cache c
 	return &d, nil
 }
 
+func executeMigration(ctx context.Context, db *sql.DB) error {
+	// TODO: Remove when we are sure we are not having goose artefacts in the db
+	// This forces an error, which indicates the migration is already applied, since the
+	// column event_nid was removed from the table
+	migrationName := "roomserver: state blocks refactor"
+	var migrationCount int
+
+	err := db.QueryRowContext(ctx, "SELECT count(*) FROM db_migrations WHERE version = $1", migrationName).Scan(&migrationCount)
+	if err != nil {
+		return err
+	}
+	if migrationCount > 0 {
+		return nil
+	}
+
+	var eventNID int
+	err = db.QueryRowContext(ctx, "SELECT event_nid FROM roomserver_state_block LIMIT 1;").Scan(&eventNID)
+	if err == nil {
+		m := sqlutil.NewMigrator(db)
+		m.AddMigrations(sqlutil.Migration{
+			Version: migrationName,
+			Up:      deltas.UpStateBlocksRefactor,
+		})
+		if err = m.Up(ctx); err != nil {
+			return err
+		}
+	} else {
+		switch e := err.(type) {
+		case *sqlite3.Error:
+			// ignore "no such column" errors, as this is expected at this point
+			if !strings.Contains(e.Error(), "no such column") {
+				return err
+			}
+
+			// reset the error to nil, so the deferred function will insert the migration
+			if err = sqlutil.InsertMigration(ctx, db, migrationName); err != nil {
+				// not a fatal error, log and continue
+				logrus.WithError(err).Warnf("unable to manually insert migration '%s'", migrationName)
+			}
+		default:
+			return err
+		}
+	}
+	return nil
+}
+
 func (d *Database) create(db *sql.DB) error {
 	if err := CreateEventStateKeysTable(db); err != nil {
 		return err