diff --git a/pkg/core/blockchain.go b/pkg/core/blockchain.go
index a08375b81..041888e3a 100644
--- a/pkg/core/blockchain.go
+++ b/pkg/core/blockchain.go
@@ -67,9 +67,6 @@ const (
 	// stateJumpStarted means that state jump was just initiated, but outdated storage items
 	// were not yet removed.
 	stateJumpStarted
-	// oldStorageItemsRemoved means that outdated contract storage items were removed, but
-	// new storage items were not yet saved.
-	oldStorageItemsRemoved
 	// newStorageItemsAdded means that contract storage items are up-to-date with the current
 	// state.
 	newStorageItemsAdded
@@ -354,6 +351,9 @@ func (bc *Blockchain) init() error {
 	bc.dao.Version = ver
 	bc.persistent.Version = ver
 
+	// Always try to remove garbage. If there is nothing to do, it will exit quickly.
+	go bc.removeOldStorageItems()
+
 	// At this point there was no version found in the storage which
 	// implies a creating fresh storage with the version specified
 	// and the genesis block as first block.
@@ -478,6 +478,26 @@ func (bc *Blockchain) init() error {
 	return bc.updateExtensibleWhitelist(bHeight)
 }
 
+func (bc *Blockchain) removeOldStorageItems() {
+	_, err := bc.dao.Store.Get(storage.SYSCleanStorage.Bytes())
+	if err != nil {
+		return
+	}
+
+	b := bc.dao.Store.Batch()
+	prefix := statesync.TemporaryPrefix(bc.dao.Version.StoragePrefix)
+	bc.dao.Store.Seek([]byte{byte(prefix)}, func(k, _ []byte) {
+		// #1468, but don't need to copy here, because it is done by Store.
+		b.Delete(k)
+	})
+	b.Delete(storage.SYSCleanStorage.Bytes())
+
+	err = bc.dao.Store.PutBatch(b)
+	if err != nil {
+		bc.log.Error("failed to remove old storage items", zap.Error(err))
+	}
+}
+
 // jumpToState is an atomic operation that changes Blockchain state to the one
 // specified by the state sync point p. All the data needed for the jump must be
 // collected by the state sync module.
@@ -509,20 +529,6 @@ func (bc *Blockchain) jumpToStateInternal(p uint32, stage stateJumpStage) error
 		}
 		fallthrough
 	case stateJumpStarted:
-		// Replace old storage items by new ones, it should be done step-by step.
-		// Firstly, remove all old genesis-related items.
-		b := bc.dao.Store.Batch()
-		bc.dao.Store.Seek([]byte{byte(bc.dao.Version.StoragePrefix)}, func(k, _ []byte) {
-			// #1468, but don't need to copy here, because it is done by Store.
-			b.Delete(k)
-		})
-		b.Put(jumpStageKey, []byte{byte(oldStorageItemsRemoved)})
-		err := bc.dao.Store.PutBatch(b)
-		if err != nil {
-			return fmt.Errorf("failed to store state jump stage: %w", err)
-		}
-		fallthrough
-	case oldStorageItemsRemoved:
 		newPrefix := statesync.TemporaryPrefix(bc.dao.Version.StoragePrefix)
 		v, err := bc.dao.GetVersion()
 		if err != nil {
@@ -538,6 +544,14 @@ func (bc *Blockchain) jumpToStateInternal(p uint32, stage stateJumpStage) error
 		if err != nil {
 			return fmt.Errorf("failed to store state jump stage: %w", err)
 		}
+
+		err = bc.dao.Store.Put(storage.SYSCleanStorage.Bytes(), []byte{})
+		if err != nil {
+			return fmt.Errorf("failed to store clean storage flag: %w", err)
+		}
+
+		go bc.removeOldStorageItems()
+
 		fallthrough
 	case newStorageItemsAdded:
 		// After current state is updated, we need to remove outdated state-related data if so.
diff --git a/pkg/core/blockchain_test.go b/pkg/core/blockchain_test.go
index a1c20be2a..2c69760e5 100644
--- a/pkg/core/blockchain_test.go
+++ b/pkg/core/blockchain_test.go
@@ -1816,7 +1816,7 @@ func TestBlockchain_InitWithIncompleteStateJump(t *testing.T) {
 		require.NoError(t, bcSpout.dao.Store.Put(storage.SYSStateSyncPoint.Bytes(), point))
 		checkNewBlockchainErr(t, boltCfg, bcSpout.dao.Store, true)
 	})
-	for _, stage := range []stateJumpStage{stateJumpStarted, oldStorageItemsRemoved, newStorageItemsAdded, genesisStateRemoved, 0x03} {
+	for _, stage := range []stateJumpStage{stateJumpStarted, newStorageItemsAdded, genesisStateRemoved, 0x03} {
 		t.Run(fmt.Sprintf("state jump stage %d", stage), func(t *testing.T) {
 			require.NoError(t, bcSpout.dao.Store.Put(storage.SYSStateJumpStage.Bytes(), []byte{byte(stage)}))
 			point := make([]byte, 4)
diff --git a/pkg/core/statesync_test.go b/pkg/core/statesync_test.go
index 7f7803d89..3b802b757 100644
--- a/pkg/core/statesync_test.go
+++ b/pkg/core/statesync_test.go
@@ -2,6 +2,7 @@ package core
 
 import (
 	"testing"
+	"time"
 
 	"github.com/nspcc-dev/neo-go/pkg/config"
 	"github.com/nspcc-dev/neo-go/pkg/core/block"
@@ -441,9 +442,13 @@ func TestStateSyncModule_RestoreBasicChain(t *testing.T) {
 	require.ElementsMatch(t, expected, actual)
 
 	// no temp items should be left
-	bcBolt.dao.Store.Seek(storage.STStorage.Bytes(), func(k, v []byte) {
-		t.Fatal("temp storage items are found")
-	})
+	require.Eventually(t, func() bool {
+		var haveItems bool
+		bcBolt.dao.Store.Seek(storage.STStorage.Bytes(), func(_, _ []byte) {
+			haveItems = true
+		})
+		return !haveItems
+	}, time.Second*5, time.Millisecond*100)
 	bcBolt.Close()
 
 	// Check restoring with new prefix.
diff --git a/pkg/core/storage/store.go b/pkg/core/storage/store.go
index ff9abd3c3..20c9be321 100644
--- a/pkg/core/storage/store.go
+++ b/pkg/core/storage/store.go
@@ -29,6 +29,7 @@ const (
 	SYSStateSyncCurrentBlockHeight KeyPrefix = 0xc2
 	SYSStateSyncPoint              KeyPrefix = 0xc3
 	SYSStateJumpStage              KeyPrefix = 0xc4
+	SYSCleanStorage                KeyPrefix = 0xc5
 	SYSVersion                     KeyPrefix = 0xf0
 )