diff --git a/syncapi/storage/postgres/deltas/20201211_sequences.go b/syncapi/storage/postgres/deltas/20201211_sequences.go
index e43d2ff21..013ddca7c 100644
--- a/syncapi/storage/postgres/deltas/20201211_sequences.go
+++ b/syncapi/storage/postgres/deltas/20201211_sequences.go
@@ -17,8 +17,19 @@ package deltas
 import (
 	"database/sql"
 	"fmt"
+
+	"github.com/matrix-org/dendrite/internal/sqlutil"
+	"github.com/pressly/goose"
 )
 
+func LoadFromGoose() {
+	goose.AddMigration(UpFixSequences, DownFixSequences)
+}
+
+func LoadFixSequences(m *sqlutil.Migrations) {
+	m.AddMigration(UpFixSequences, DownFixSequences)
+}
+
 func UpFixSequences(tx *sql.Tx) error {
 	_, err := tx.Exec(`
 		-- We need to delete all of the existing receipts because the indexes
diff --git a/syncapi/storage/postgres/deltas/deltas.go b/syncapi/storage/sqlite3/deltas/20201211_sequences.go
similarity index 52%
rename from syncapi/storage/postgres/deltas/deltas.go
rename to syncapi/storage/sqlite3/deltas/20201211_sequences.go
index 8c19e9dcc..7211d96f4 100644
--- a/syncapi/storage/postgres/deltas/deltas.go
+++ b/syncapi/storage/sqlite3/deltas/20201211_sequences.go
@@ -15,6 +15,9 @@
 package deltas
 
 import (
+	"database/sql"
+	"fmt"
+
 	"github.com/matrix-org/dendrite/internal/sqlutil"
 	"github.com/pressly/goose"
 )
@@ -26,3 +29,29 @@ func LoadFromGoose() {
 func LoadFixSequences(m *sqlutil.Migrations) {
 	m.AddMigration(UpFixSequences, DownFixSequences)
 }
+
+func UpFixSequences(tx *sql.Tx) error {
+	_, err := tx.Exec(`
+		-- We need to delete all of the existing receipts because the indexes
+		-- will be wrong, and we'll get primary key violations if we try to
+		-- reuse existing stream IDs from a different sequence.
+		DELETE FROM syncapi_receipts;
+	`)
+	if err != nil {
+		return fmt.Errorf("failed to execute upgrade: %w", err)
+	}
+	return nil
+}
+
+func DownFixSequences(tx *sql.Tx) error {
+	_, err := tx.Exec(`
+		-- We need to delete all of the existing receipts because the indexes
+		-- will be wrong, and we'll get primary key violations if we try to
+		-- reuse existing stream IDs from a different sequence.
+		DELETE FROM syncapi_receipts;
+	`)
+	if err != nil {
+		return fmt.Errorf("failed to execute downgrade: %w", err)
+	}
+	return nil
+}
diff --git a/syncapi/storage/sqlite3/syncserver.go b/syncapi/storage/sqlite3/syncserver.go
index 7df71b384..f07359e7a 100644
--- a/syncapi/storage/sqlite3/syncserver.go
+++ b/syncapi/storage/sqlite3/syncserver.go
@@ -25,6 +25,7 @@ import (
 	"github.com/matrix-org/dendrite/internal/sqlutil"
 	"github.com/matrix-org/dendrite/setup/config"
 	"github.com/matrix-org/dendrite/syncapi/storage/shared"
+	"github.com/matrix-org/dendrite/syncapi/storage/sqlite3/deltas"
 )
 
 // SyncServerDatasource represents a sync server datasource which manages
@@ -46,13 +47,13 @@ func NewDatabase(dbProperties *config.DatabaseOptions) (*SyncServerDatasource, e
 		return nil, err
 	}
 	d.writer = sqlutil.NewExclusiveWriter()
-	if err = d.prepare(); err != nil {
+	if err = d.prepare(dbProperties); err != nil {
 		return nil, err
 	}
 	return &d, nil
 }
 
-func (d *SyncServerDatasource) prepare() (err error) {
+func (d *SyncServerDatasource) prepare(dbProperties *config.DatabaseOptions) (err error) {
 	if err = d.PartitionOffsetStatements.Prepare(d.db, d.writer, "syncapi"); err != nil {
 		return err
 	}
@@ -99,6 +100,11 @@ func (d *SyncServerDatasource) prepare() (err error) {
 	if err != nil {
 		return err
 	}
+	m := sqlutil.NewMigrations()
+	deltas.LoadFixSequences(m)
+	if err = m.RunDeltas(d.db, dbProperties); err != nil {
+		return err
+	}
 	d.Database = shared.Database{
 		DB:                  d.db,
 		Writer:              d.writer,