diff --git a/raftwal/fsm.go b/raftwal/fsm.go
index 00c2c0e54..81d9890d4 100644
--- a/raftwal/fsm.go
+++ b/raftwal/fsm.go
@@ -188,11 +188,11 @@ func (fsm *BalloonFSM) Snapshot() (raft.FSMSnapshot, error) {
 	fsm.restoreMu.Lock()
 	defer fsm.restoreMu.Unlock()
 
-	version, err := fsm.store.GetLastVersion()
+	id, err := fsm.store.Snapshot()
 	if err != nil {
 		return nil, err
 	}
-	log.Debugf("Generating snapshot until version: %d (balloon version %d)", version, fsm.balloon.Version())
+	log.Debugf("Generating snapshot until version: %d (balloon version %d)", id, fsm.balloon.Version())
 
 	// Copy the node metadata.
 	meta, err := json.Marshal(fsm.meta)
@@ -200,8 +200,8 @@ func (fsm *BalloonFSM) Snapshot() (raft.FSMSnapshot, error) {
 		log.Debugf("failed to encode meta for snapshot: %s", err.Error())
 		return nil, err
 	}
-
-	return &fsmSnapshot{lastVersion: version, store: fsm.store, meta: meta}, nil
+	// change lastVersion by checkpoint structure
+	return &fsmSnapshot{id: id, store: fsm.store, meta: meta}, nil
 }
 
 // Restore restores the node to a previous state.
diff --git a/raftwal/snapshot.go b/raftwal/snapshot.go
index d3ef66b9e..233d1a058 100644
--- a/raftwal/snapshot.go
+++ b/raftwal/snapshot.go
@@ -23,16 +23,16 @@ import (
 )
 
 type fsmSnapshot struct {
-	lastVersion uint64
-	store       storage.ManagedStore
-	meta        []byte
+	id    uint64
+	store storage.ManagedStore
+	meta  []byte
 }
 
 // Persist writes the snapshot to the given sink.
 func (f *fsmSnapshot) Persist(sink raft.SnapshotSink) error {
 	log.Debug("Persisting snapshot...")
 	err := func() error {
-		if err := f.store.Backup(sink, f.lastVersion); err != nil {
+		if err := f.store.Backup(sink, f.id); err != nil {
 			return err
 		}
 		return sink.Close()
diff --git a/storage/badger/badger_store.go b/storage/badger/badger_store.go
index 72d792aac..794a78fba 100644
--- a/storage/badger/badger_store.go
+++ b/storage/badger/badger_store.go
@@ -335,7 +335,11 @@ func (s *BadgerStore) Load(r io.Reader) error {
 	return s.db.Load(r)
 }
 
-func (s *BadgerStore) GetLastVersion() (uint64, error) {
+// Take a snapshot of the store, and returns and id
+// to be used in the back up process. The state of the
+// snapshot is stored in the store instance.
+// In badger the id corresponds to the last version stored.
+func (s *BadgerStore) Snapshot() (uint64, error) {
 	var version uint64
 	err := s.db.View(func(txn *b.Txn) error {
 		opts := b.DefaultIteratorOptions
diff --git a/storage/badger/badger_store_test.go b/storage/badger/badger_store_test.go
index 4908a4971..2e5ea0e56 100644
--- a/storage/badger/badger_store_test.go
+++ b/storage/badger/badger_store_test.go
@@ -238,7 +238,7 @@ func TestBackupLoad(t *testing.T) {
 		}
 	}
 
-	version, err := store.GetLastVersion()
+	version, err := store.Snapshot()
 	require.NoError(t, err)
 
 	backupDir := mustTempDir()
@@ -251,7 +251,7 @@ func TestBackupLoad(t *testing.T) {
 	restore, recloseF := openBadgerStore(t)
 	defer recloseF()
 	restore.Load(backupFile)
-	reversion, err := store.GetLastVersion()
+	reversion, err := store.Snapshot()
 
 	require.NoError(t, err)
 	require.Equal(t, reversion, version, "Error in restored version")
diff --git a/storage/rocks/rocksdb_store.go b/storage/rocks/rocksdb_store.go
index 81e6b7e72..dad1aa3d8 100644
--- a/storage/rocks/rocksdb_store.go
+++ b/storage/rocks/rocksdb_store.go
@@ -19,8 +19,8 @@ import (
 	"bufio"
 	"bytes"
 	"encoding/binary"
+	"fmt"
 	"io"
-	"io/ioutil"
 	"os"
 
 	"github.com/bbva/qed/rocksdb"
@@ -30,6 +30,15 @@ import (
 
 type RocksDBStore struct {
 	db *rocksdb.DB
+
+	// checkpoints are stored in a path on the same
+	// folder as the database, so rocksdb uses hardlinks instead
+	// of copies
+	checkPointPath string
+
+	// each checkpoint is created in a subdirectory
+	// inside checkPointPath folder
+	checkpoints map[uint64]string
 }
 
 type rocksdbOpts struct {
@@ -55,8 +64,17 @@ func NewRocksDBStoreOpts(opts *rocksdbOpts) (*RocksDBStore, error) {
 	if err != nil {
 		return nil, err
 	}
+	checkPointPath := opts.Path + "/checkpoints"
+	err = os.MkdirAll(checkPointPath, 0755)
+	if err != nil {
+		return nil, err
+	}
 
-	store := &RocksDBStore{db: db}
+	store := &RocksDBStore{
+		db:             db,
+		checkPointPath: checkPointPath,
+		checkpoints:    make(map[uint64]string),
+	}
 	return store, nil
 }
 
@@ -172,26 +190,32 @@ func (s RocksDBStore) Delete(prefix byte, key []byte) error {
 	return s.db.Delete(rocksdb.NewDefaultWriteOptions(), k)
 }
 
-// Backup dumps a protobuf-encoded list of all entries in the database into the
-// given writer, that are newer than the specified version.
-func (s *RocksDBStore) Backup(w io.Writer, until uint64) error {
-
+// Take a snapshot of the store, and returns and id
+// to be used in the back up process. The state of the
+// snapshot is stored in the store instance.
+func (s *RocksDBStore) Snapshot() (uint64, error) {
 	// create temp directory
-	checkDir, err := ioutil.TempDir("", "rocksdb-checkpoint")
-	if err != nil {
-		return err
-	}
+	id := uint64(len(s.checkpoints) + 1)
+	checkDir := fmt.Sprintf("%s/rocksdb-checkpoint-%d", s.checkPointPath, id)
 	os.RemoveAll(checkDir)
 
 	// create checkpoint
 	checkpoint, err := s.db.NewCheckpoint()
 	if err != nil {
-		return err
+		return 0, err
 	}
 	defer checkpoint.Destroy()
-
 	checkpoint.CreateCheckpoint(checkDir, 0)
-	defer os.RemoveAll(checkDir)
+
+	s.checkpoints[id] = checkDir
+	return id, nil
+}
+
+// Backup dumps a protobuf-encoded list of all entries in the database into the
+// given writer, that are newer than the specified version.
+func (s *RocksDBStore) Backup(w io.Writer, id uint64) error {
+
+	checkDir := s.checkpoints[id]
 
 	// open db for read-only
 	opts := rocksdb.NewDefaultOptions()
@@ -223,6 +247,13 @@ func (s *RocksDBStore) Backup(w io.Writer, until uint64) error {
 		}
 	}
 
+	// remove checkpoint from list
+	// order must be maintained,
+	delete(s.checkpoints, id)
+
+	// clean up only after we succesfully backup
+	os.RemoveAll(checkDir)
+
 	return nil
 }
 
diff --git a/storage/rocks/rocksdb_store_test.go b/storage/rocks/rocksdb_store_test.go
index 0bc8a23c8..832767a8e 100644
--- a/storage/rocks/rocksdb_store_test.go
+++ b/storage/rocks/rocksdb_store_test.go
@@ -207,7 +207,9 @@ func TestBackupLoad(t *testing.T) {
 
 	// create backup
 	ioBuf := bytes.NewBufferString("")
-	require.NoError(t, store.Backup(ioBuf, 0))
+	id, err := store.Snapshot()
+	require.Nil(t, err)
+	require.NoError(t, store.Backup(ioBuf, id))
 
 	// restore backup
 	restore, recloseF := openRocksDBStore(t)
diff --git a/storage/store.go b/storage/store.go
index dd4ea1802..daa4f2172 100644
--- a/storage/store.go
+++ b/storage/store.go
@@ -47,11 +47,12 @@ type DeletableStore interface {
 	Store
 	Delete(prefix byte, key []byte) error
 }
+
 type ManagedStore interface {
 	Store
 	Backup(w io.Writer, until uint64) error
+	Snapshot() (uint64, error)
 	Load(r io.Reader) error
-	GetLastVersion() (uint64, error)
 }
 
 type Mutation struct {