diff --git a/pkg/local_object_storage/metabase/upgrade.go b/pkg/local_object_storage/metabase/upgrade.go
new file mode 100644
index 000000000..715ef22cf
--- /dev/null
+++ b/pkg/local_object_storage/metabase/upgrade.go
@@ -0,0 +1,248 @@
+package meta
+
+import (
+	"bytes"
+	"context"
+	"encoding/binary"
+	"errors"
+	"fmt"
+	"os"
+	"strconv"
+	"time"
+
+	objectV2 "git.frostfs.info/TrueCloudLab/frostfs-api-go/v2/object"
+	cid "git.frostfs.info/TrueCloudLab/frostfs-sdk-go/container/id"
+	oid "git.frostfs.info/TrueCloudLab/frostfs-sdk-go/object/id"
+	"go.etcd.io/bbolt"
+	"golang.org/x/sync/errgroup"
+)
+
+var updates = map[uint64]func(ctx context.Context, db *bbolt.DB) error{
+	2: upgradeFromV2ToV3,
+}
+
+var errFailedToUpgradeDatabaseNotOpen = errors.New("failed to upgrade metabase: database not open")
+
+func (db *DB) Upgrade(ctx context.Context, compact bool) error {
+	db.modeMtx.Lock()
+	defer db.modeMtx.Unlock()
+
+	if db.mode.NoMetabase() {
+		return ErrDegradedMode
+	} else if db.mode.ReadOnly() {
+		return ErrReadOnlyMode
+	}
+
+	if db.boltDB == nil {
+		return errFailedToUpgradeDatabaseNotOpen
+	}
+
+	var version uint64
+	if err := db.boltDB.View(func(tx *bbolt.Tx) error {
+		var e error
+		version, e = currentVersion(tx)
+		return e
+	}); err != nil {
+		return err
+	}
+	updater, found := updates[version]
+	if !found {
+		return fmt.Errorf("unsupported version %d: no update available", version)
+	}
+	if err := updater(ctx, db.boltDB); err != nil {
+		return fmt.Errorf("failed to update metabase schema: %w", err)
+	}
+	if compact {
+		err := db.compact()
+		if err != nil {
+			return fmt.Errorf("failed to compact metabase: %w", err)
+		}
+	}
+	return nil
+}
+
+func (db *DB) compact() error {
+	tmpFileName := db.info.Path + "." + time.Now().Format(time.RFC3339)
+	dst, err := bbolt.Open(tmpFileName, db.info.Permission, db.boltOptions)
+	if err != nil {
+		return fmt.Errorf("can't open new metabase to compact: %w", err)
+	}
+	if err := bbolt.Compact(dst, db.boltDB, 256<<20); err != nil {
+		return fmt.Errorf("failed to compact metabase: %w", errors.Join(err, dst.Close(), os.Remove(tmpFileName)))
+	}
+	if err := dst.Close(); err != nil {
+		return fmt.Errorf("failed to close compacted metabase: %w", errors.Join(err, os.Remove(tmpFileName)))
+	}
+	if err := db.boltDB.Close(); err != nil {
+		return fmt.Errorf("failed to close source metabase: %w", errors.Join(err, os.Remove(tmpFileName)))
+	}
+	db.boltDB = nil
+	db.initialized = false
+	if err := os.Rename(tmpFileName, db.info.Path); err != nil {
+		return fmt.Errorf("failed to replace source metabase with compacted: %w", errors.Join(err, os.Remove(tmpFileName)))
+	}
+	return db.openBolt()
+}
+
+func upgradeFromV2ToV3(ctx context.Context, db *bbolt.DB) error {
+	if err := createExpirationEpochBuckets(ctx, db); err != nil {
+		return err
+	}
+	if err := dropUserAttributes(ctx, db); err != nil {
+		return err
+	}
+	if err := dropOwnerIDIndex(ctx, db); err != nil {
+		return err
+	}
+	return dropPayloadChecksumIndex(ctx, db)
+}
+
+type objectIDToExpEpoch struct {
+	containerID     cid.ID
+	objectID        oid.ID
+	expirationEpoch uint64
+}
+
+func createExpirationEpochBuckets(ctx context.Context, db *bbolt.DB) error {
+	if err := db.Update(func(tx *bbolt.Tx) error {
+		_, err := tx.CreateBucketIfNotExists(expEpochToObjectBucketName)
+		return err
+	}); err != nil {
+		return err
+	}
+
+	objects := make(chan objectIDToExpEpoch, 1000)
+	defer func() {
+		close(objects)
+	}()
+
+	eg, ctx := errgroup.WithContext(ctx)
+	eg.Go(func() error {
+		prefix := []byte{userAttributePrefix}
+		return db.View(func(tx *bbolt.Tx) error {
+			userAttrCursor := tx.Cursor()
+			for userAttrKey, _ := userAttrCursor.Seek(prefix); userAttrKey != nil && bytes.HasPrefix(userAttrKey, prefix); userAttrKey, _ = userAttrCursor.Next() {
+				select {
+				case <-ctx.Done():
+					return ctx.Err()
+				default:
+				}
+
+				if len(userAttrKey) <= 1+cidSize {
+					continue
+				}
+				attributeKey := string(userAttrKey[1+cidSize:])
+				if attributeKey != objectV2.SysAttributeExpEpochNeoFS && attributeKey != objectV2.SysAttributeExpEpoch {
+					continue
+				}
+
+				var containerID cid.ID
+				if err := containerID.Decode(userAttrKey[1 : 1+cidSize]); err != nil {
+					return fmt.Errorf("failed to decode container id from user attribute bucket: %w", err)
+				}
+
+				b := tx.Bucket(userAttrKey)
+				return b.ForEachBucket(func(expKey []byte) error {
+					select {
+					case <-ctx.Done():
+						return ctx.Err()
+					default:
+					}
+
+					expirationEpoch, err := strconv.ParseUint(string(expKey), 10, 64)
+					if err != nil {
+						return fmt.Errorf("could not parse expiration epoch: %w", err)
+					}
+					expirationEpochBucket := b.Bucket(expKey)
+					return expirationEpochBucket.ForEach(func(k, _ []byte) error {
+						var objectID oid.ID
+						if err := objectID.Decode(k); err != nil {
+							return fmt.Errorf("failed to decode object id from container '%s' expiration epoch %d: %w", containerID, expirationEpoch, err)
+						}
+						select {
+						case <-ctx.Done():
+							return ctx.Err()
+						case objects <- objectIDToExpEpoch{
+							containerID:     containerID,
+							objectID:        objectID,
+							expirationEpoch: expirationEpoch,
+						}:
+							return nil
+						}
+					})
+				})
+			}
+			return nil
+		})
+	})
+	eg.Go(func() error {
+		select {
+		case <-ctx.Done():
+			return ctx.Err()
+		case obj := <-objects:
+			return db.Update(func(tx *bbolt.Tx) error {
+				if err := putUniqueIndexItem(tx, namedBucketItem{
+					name: expEpochToObjectBucketName,
+					key:  expirationEpochKey(obj.expirationEpoch, obj.containerID, obj.objectID),
+					val:  zeroValue,
+				}); err != nil {
+					return err
+				}
+				val := make([]byte, epochSize)
+				binary.LittleEndian.PutUint64(val, obj.expirationEpoch)
+				return putUniqueIndexItem(tx, namedBucketItem{
+					name: objectToExpirationEpochBucketName(obj.containerID, make([]byte, bucketKeySize)),
+					key:  objectKey(obj.objectID, make([]byte, objectKeySize)),
+					val:  val,
+				})
+			})
+		}
+	})
+	return eg.Wait()
+}
+
+func dropUserAttributes(ctx context.Context, db *bbolt.DB) error {
+	return dropBucketsByPrefix(ctx, db, []byte{userAttributePrefix})
+}
+
+func dropOwnerIDIndex(ctx context.Context, db *bbolt.DB) error {
+	return dropBucketsByPrefix(ctx, db, []byte{ownerPrefix})
+}
+
+func dropPayloadChecksumIndex(ctx context.Context, db *bbolt.DB) error {
+	return dropBucketsByPrefix(ctx, db, []byte{payloadHashPrefix})
+}
+
+func dropBucketsByPrefix(ctx context.Context, db *bbolt.DB, prefix []byte) error {
+	const batch = 100
+	for {
+		select {
+		case <-ctx.Done():
+			return ctx.Err()
+		default:
+		}
+		var keys [][]byte
+		if err := db.View(func(tx *bbolt.Tx) error {
+			c := tx.Cursor()
+			for k, _ := c.Seek(prefix); k != nil && bytes.HasPrefix(k, prefix) && len(keys) < batch; k, _ = c.Next() {
+				keys = append(keys, bytes.Clone(k))
+			}
+			return nil
+		}); err != nil {
+			return err
+		}
+		if len(keys) == 0 {
+			return nil
+		}
+		if err := db.Update(func(tx *bbolt.Tx) error {
+			for _, k := range keys {
+				if err := tx.DeleteBucket(k); err != nil {
+					return err
+				}
+			}
+			return nil
+		}); err != nil {
+			return err
+		}
+	}
+}
diff --git a/pkg/local_object_storage/metabase/util.go b/pkg/local_object_storage/metabase/util.go
index 9134616fe..eef7210dc 100644
--- a/pkg/local_object_storage/metabase/util.go
+++ b/pkg/local_object_storage/metabase/util.go
@@ -94,11 +94,13 @@ const (
 	// ownerPrefix was used for prefixing FKBT index buckets mapping owner to object IDs.
 	// Key: owner ID
 	// Value: bucket containing object IDs as keys
-	_
+	// removed in version 3
+	ownerPrefix
 	// userAttributePrefix was used for prefixing FKBT index buckets containing objects.
 	// Key: attribute value
 	// Value: bucket containing object IDs as keys
-	_
+	// removed in version 3
+	userAttributePrefix
 
 	// ====================
 	// List index buckets.
@@ -107,7 +109,8 @@ const (
 	// payloadHashPrefix was used for prefixing List index buckets mapping payload hash to a list of object IDs.
 	//  Key: payload hash
 	//  Value: list of object IDs
-	_
+	// removed in version 3
+	payloadHashPrefix
 	// parentPrefix is used for prefixing List index buckets mapping parent ID to a list of children IDs.
 	//  Key: parent ID
 	//  Value: list of object IDs
diff --git a/pkg/local_object_storage/metabase/version.go b/pkg/local_object_storage/metabase/version.go
index bb2b66d9b..523c95fd2 100644
--- a/pkg/local_object_storage/metabase/version.go
+++ b/pkg/local_object_storage/metabase/version.go
@@ -59,3 +59,15 @@ func updateVersion(tx *bbolt.Tx, version uint64) error {
 	}
 	return b.Put(versionKey, data)
 }
+
+func currentVersion(tx *bbolt.Tx) (uint64, error) {
+	b := tx.Bucket(shardInfoBucket)
+	if b == nil {
+		return 0, fmt.Errorf("version undefined: no info bucket")
+	}
+	data := b.Get(versionKey)
+	if len(data) != 8 {
+		return 0, fmt.Errorf("version undefined: invalid version data lenght %d", len(data))
+	}
+	return binary.LittleEndian.Uint64(data), nil
+}
diff --git a/pkg/local_object_storage/shard/control.go b/pkg/local_object_storage/shard/control.go
index 936a506c0..68d2362f2 100644
--- a/pkg/local_object_storage/shard/control.go
+++ b/pkg/local_object_storage/shard/control.go
@@ -172,7 +172,13 @@ func (s *Shard) initializeComponents(m mode.Mode) error {
 		if err := component.Init(); err != nil {
 			if component == s.metaBase {
 				if errors.Is(err, meta.ErrOutdatedVersion) {
-					return fmt.Errorf("metabase initialization: %w", err)
+					err = s.metaBase.Upgrade(context.TODO(), true) // TODO replace with config variable
+					if err == nil {
+						err = s.metaBase.Init()
+					}
+				}
+				if err == nil {
+					continue
 				}
 
 				err = s.handleMetabaseFailure("init", err)