diff --git a/lib/storage/index_db.go b/lib/storage/index_db.go
index b4511d4cca..3c0f198bdd 100644
--- a/lib/storage/index_db.go
+++ b/lib/storage/index_db.go
@@ -2391,7 +2391,9 @@ func (tmm *tagToMetricIDsRowsMerger) flushPendingMetricIDs(dstData []byte, dstIt
 	}
 	// Use sort.Sort instead of sort.Slice in order to reduce memory allocations.
 	sort.Sort(&tmm.pendingMetricIDs)
+	tmm.pendingMetricIDs = removeDuplicateMetricIDs(tmm.pendingMetricIDs)
 
+	// Marshal pendingMetricIDs
 	dstDataLen := len(dstData)
 	dstData = marshalCommonPrefix(dstData, nsPrefixTagToMetricIDs, mp.AccountID, mp.ProjectID)
 	dstData = mp.Tag.Marshal(dstData)
@@ -2403,6 +2405,33 @@ func (tmm *tagToMetricIDsRowsMerger) flushPendingMetricIDs(dstData []byte, dstIt
 	return dstData, dstItems
 }
 
+func removeDuplicateMetricIDs(sortedMetricIDs []uint64) []uint64 {
+	if len(sortedMetricIDs) < 2 {
+		return sortedMetricIDs
+	}
+	prevMetricID := sortedMetricIDs[0]
+	hasDuplicates := false
+	for _, metricID := range sortedMetricIDs[1:] {
+		if prevMetricID == metricID {
+			hasDuplicates = true
+		}
+		prevMetricID = metricID
+	}
+	if !hasDuplicates {
+		return sortedMetricIDs
+	}
+	dstMetricIDs := sortedMetricIDs[:1]
+	prevMetricID = sortedMetricIDs[0]
+	for _, metricID := range sortedMetricIDs[1:] {
+		if prevMetricID == metricID {
+			continue
+		}
+		dstMetricIDs = append(dstMetricIDs, metricID)
+		prevMetricID = metricID
+	}
+	return dstMetricIDs
+}
+
 func getTagToMetricIDsRowsMerger() *tagToMetricIDsRowsMerger {
 	v := tmmPool.Get()
 	if v == nil {
diff --git a/lib/storage/index_db_test.go b/lib/storage/index_db_test.go
index 3302455eed..570424775a 100644
--- a/lib/storage/index_db_test.go
+++ b/lib/storage/index_db_test.go
@@ -15,6 +15,23 @@ import (
 	"github.com/VictoriaMetrics/VictoriaMetrics/lib/workingsetcache"
 )
 
+func TestRemoveDuplicateMetricIDs(t *testing.T) {
+	f := func(metricIDs, expectedMetricIDs []uint64) {
+		a := removeDuplicateMetricIDs(metricIDs)
+		if !reflect.DeepEqual(a, expectedMetricIDs) {
+			t.Fatalf("unexpected result from removeDuplicateMetricIDs:\ngot\n%d\nwant\n%d", a, expectedMetricIDs)
+		}
+	}
+	f(nil, nil)
+	f([]uint64{123}, []uint64{123})
+	f([]uint64{123, 123}, []uint64{123})
+	f([]uint64{123, 123, 123}, []uint64{123})
+	f([]uint64{0, 1, 1, 2}, []uint64{0, 1, 2})
+	f([]uint64{0, 0, 0, 1, 1, 2}, []uint64{0, 1, 2})
+	f([]uint64{0, 1, 1, 2, 2}, []uint64{0, 1, 2})
+	f([]uint64{0, 1, 2, 2}, []uint64{0, 1, 2})
+}
+
 func TestMarshalUnmarshalTSIDs(t *testing.T) {
 	f := func(tsids []TSID) {
 		t.Helper()