diff --git a/internal/repository/master_index.go b/internal/repository/master_index.go
index 4fdd4a0ce..660fb40aa 100644
--- a/internal/repository/master_index.go
+++ b/internal/repository/master_index.go
@@ -287,7 +287,9 @@ func (mi *MasterIndex) MergeFinalIndexes() error {
 		idx := mi.idx[i]
 		// clear reference in masterindex as it may become stale
 		mi.idx[i] = nil
-		if !idx.Final() {
+		// do not merge indexes that have no id set
+		ids, _ := idx.IDs()
+		if !idx.Final() || len(ids) == 0 {
 			newIdx = append(newIdx, idx)
 		} else {
 			err := mi.idx[0].merge(idx)
@@ -404,7 +406,13 @@ func SaveIndex(ctx context.Context, repo restic.SaverUnpacked, index *Index) (re
 		return restic.ID{}, err
 	}
 
-	return repo.SaveUnpacked(ctx, restic.IndexFile, buf.Bytes())
+	id, err := repo.SaveUnpacked(ctx, restic.IndexFile, buf.Bytes())
+	ierr := index.SetID(id)
+	if ierr != nil {
+		// logic bug
+		panic(ierr)
+	}
+	return id, err
 }
 
 // saveIndex saves all indexes in the backend.
diff --git a/internal/repository/master_index_test.go b/internal/repository/master_index_test.go
index 0aeaf5eb1..ffdaf7af9 100644
--- a/internal/repository/master_index_test.go
+++ b/internal/repository/master_index_test.go
@@ -157,16 +157,9 @@ func TestMasterMergeFinalIndexes(t *testing.T) {
 	mIdx.Insert(idx1)
 	mIdx.Insert(idx2)
 
-	finalIndexes := mIdx.FinalizeNotFinalIndexes()
+	finalIndexes, idxCount := repository.TestMergeIndex(t, mIdx)
 	rtest.Equals(t, []*repository.Index{idx1, idx2}, finalIndexes)
-
-	err := mIdx.MergeFinalIndexes()
-	if err != nil {
-		t.Fatal(err)
-	}
-
-	allIndexes := mIdx.All()
-	rtest.Equals(t, 1, len(allIndexes))
+	rtest.Equals(t, 1, idxCount)
 
 	blobCount := 0
 	for range mIdx.Each(context.TODO()) {
@@ -189,16 +182,9 @@ func TestMasterMergeFinalIndexes(t *testing.T) {
 	idx3.StorePack(blob2.PackID, []restic.Blob{blob2.Blob})
 
 	mIdx.Insert(idx3)
-	finalIndexes = mIdx.FinalizeNotFinalIndexes()
+	finalIndexes, idxCount = repository.TestMergeIndex(t, mIdx)
 	rtest.Equals(t, []*repository.Index{idx3}, finalIndexes)
-
-	err = mIdx.MergeFinalIndexes()
-	if err != nil {
-		t.Fatal(err)
-	}
-
-	allIndexes = mIdx.All()
-	rtest.Equals(t, 1, len(allIndexes))
+	rtest.Equals(t, 1, idxCount)
 
 	// Index should have same entries as before!
 	blobs = mIdx.Lookup(bhInIdx1)
diff --git a/internal/repository/repository.go b/internal/repository/repository.go
index 77cf01989..01a7cad8a 100644
--- a/internal/repository/repository.go
+++ b/internal/repository/repository.go
@@ -582,12 +582,6 @@ func (r *Repository) LoadIndex(ctx context.Context) error {
 		if err != nil {
 			return err
 		}
-
-		_, err = idx.IDs()
-		if err != nil {
-			return err
-		}
-
 		r.idx.Insert(idx)
 		return nil
 	})
diff --git a/internal/repository/testing.go b/internal/repository/testing.go
index 05dfab64d..a24148a1b 100644
--- a/internal/repository/testing.go
+++ b/internal/repository/testing.go
@@ -132,3 +132,13 @@ func BenchmarkAllVersions(b *testing.B, bench VersionedBenchmark) {
 		})
 	}
 }
+
+func TestMergeIndex(t testing.TB, mi *MasterIndex) ([]*Index, int) {
+	finalIndexes := mi.FinalizeNotFinalIndexes()
+	for _, idx := range finalIndexes {
+		test.OK(t, idx.SetID(restic.NewRandomID()))
+	}
+
+	test.OK(t, mi.MergeFinalIndexes())
+	return finalIndexes, len(mi.idx)
+}