diff --git a/keyserver/storage/postgres/key_changes_table.go b/keyserver/storage/postgres/key_changes_table.go
index 004f15d82..5ad5a9749 100644
--- a/keyserver/storage/postgres/key_changes_table.go
+++ b/keyserver/storage/postgres/key_changes_table.go
@@ -19,6 +19,7 @@ import (
 	"database/sql"
 
 	"github.com/lib/pq"
+	"github.com/sirupsen/logrus"
 
 	"github.com/matrix-org/dendrite/internal"
 	"github.com/matrix-org/dendrite/internal/sqlutil"
@@ -63,30 +64,54 @@ func NewPostgresKeyChangesTable(db *sql.DB) (tables.KeyChanges, error) {
 		return s, err
 	}
 
+	if err = executeMigration(context.Background(), db); err != nil {
+		return nil, err
+	}
+	return s, 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 partition was removed from the table
-	var count int
-	err = db.QueryRow("SELECT partition FROM keyserver_key_changes LIMIT 1;").Scan(&count)
+	migrationName := "keyserver: refactor key changes"
+	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 partition int
+	err = db.QueryRowContext(ctx, "SELECT partition FROM keyserver_key_changes LIMIT 1;").Scan(&partition)
 	if err == nil {
 		m := sqlutil.NewMigrator(db)
 		m.AddMigrations(sqlutil.Migration{
-			Version: "keyserver: refactor key changes",
+			Version: migrationName,
 			Up:      deltas.UpRefactorKeyChanges,
 		})
-		return s, m.Up(context.Background())
+		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 nil, err
+				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 nil, err
+			return err
 		}
 	}
-	return s, nil
+	return nil
 }
 
 func (s *keyChangesStatements) Prepare() (err error) {
diff --git a/keyserver/storage/sqlite3/key_changes_table.go b/keyserver/storage/sqlite3/key_changes_table.go
index 217fa7a5d..f3d743cac 100644
--- a/keyserver/storage/sqlite3/key_changes_table.go
+++ b/keyserver/storage/sqlite3/key_changes_table.go
@@ -17,6 +17,10 @@ package sqlite3
 import (
 	"context"
 	"database/sql"
+	"strings"
+
+	"github.com/mattn/go-sqlite3"
+	"github.com/sirupsen/logrus"
 
 	"github.com/matrix-org/dendrite/internal"
 	"github.com/matrix-org/dendrite/internal/sqlutil"
@@ -58,23 +62,60 @@ func NewSqliteKeyChangesTable(db *sql.DB) (tables.KeyChanges, error) {
 	if err != nil {
 		return s, err
 	}
-	// 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 partition was removed from the table
-	var count int
-	err = db.QueryRow("SELECT partition FROM keyserver_key_changes LIMIT 1;").Scan(&count)
-	if err == nil {
-		m := sqlutil.NewMigrator(db)
-		m.AddMigrations(sqlutil.Migration{
-			Version: "keyserver: refactor key changes",
-			Up:      deltas.UpRefactorKeyChanges,
-		})
-		return s, m.Up(context.Background())
+
+	if err = executeMigration(context.Background(), db); err != nil {
+		return nil, err
 	}
 
 	return s, 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 partition was removed from the table
+	migrationName := "keyserver: refactor key changes"
+	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 partition int
+	err = db.QueryRowContext(ctx, "SELECT partition FROM keyserver_key_changes LIMIT 1;").Scan(&partition)
+	if err == nil {
+		m := sqlutil.NewMigrator(db)
+		m.AddMigrations(sqlutil.Migration{
+			Version: migrationName,
+			Up:      deltas.UpRefactorKeyChanges,
+		})
+		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 (s *keyChangesStatements) Prepare() (err error) {
 	if s.upsertKeyChangeStmt, err = s.db.Prepare(upsertKeyChangeSQL); err != nil {
 		return err