diff --git a/internal/datacoord/index_meta.go b/internal/datacoord/index_meta.go
index 4f75c3799a39f..cfc2a746c7be9 100644
--- a/internal/datacoord/index_meta.go
+++ b/internal/datacoord/index_meta.go
@@ -638,7 +638,7 @@ func (m *indexMeta) GetIndexedSegments(collectionID int64, segmentIDs, fieldIDs
 	matchedFields := typeutil.NewUniqueSet()
 
 	targetIndices := lo.Filter(lo.Values(fieldIndexes), func(index *model.Index, _ int) bool {
-		return fieldIDSet.Contain(index.FieldID)
+		return fieldIDSet.Contain(index.FieldID) && !index.IsDeleted
 	})
 	for _, index := range targetIndices {
 		matchedFields.Insert(index.FieldID)
@@ -652,10 +652,6 @@ func (m *indexMeta) GetIndexedSegments(collectionID int64, segmentIDs, fieldIDs
 	checkSegmentState := func(indexes *typeutil.ConcurrentMap[UniqueID, *model.SegmentIndex]) bool {
 		indexedFields := 0
 		for _, index := range targetIndices {
-			if !fieldIDSet.Contain(index.FieldID) || index.IsDeleted {
-				continue
-			}
-
 			if segIdx, ok := indexes.Get(index.IndexID); ok && segIdx.IndexState == commonpb.IndexState_Finished {
 				indexedFields += 1
 			}
diff --git a/internal/datacoord/index_meta_test.go b/internal/datacoord/index_meta_test.go
index ec578bf5455c8..0ee074ede2c29 100644
--- a/internal/datacoord/index_meta_test.go
+++ b/internal/datacoord/index_meta_test.go
@@ -817,6 +817,35 @@ func TestMeta_GetIndexedSegment(t *testing.T) {
 		segments := m.GetIndexedSegments(collID+1, []int64{segID}, []int64{fieldID})
 		assert.Len(t, segments, 0)
 	})
+
+	t.Run("with deleted index entries", func(t *testing.T) {
+		// Simulate drop+create index cycles: add deleted index entries for the same field.
+		// Previously, deleted entries inflated len(targetIndices), causing the indexed check
+		// to always fail (indexedFields=1 != len(targetIndices)=N).
+		deletedIndexID1 := indexID + 100
+		deletedIndexID2 := indexID + 200
+		m.indexes[collID][deletedIndexID1] = &model.Index{
+			CollectionID: collID,
+			FieldID:      fieldID,
+			IndexID:      deletedIndexID1,
+			IndexName:    "old_idx_1",
+			IsDeleted:    true,
+		}
+		m.indexes[collID][deletedIndexID2] = &model.Index{
+			CollectionID: collID,
+			FieldID:      fieldID,
+			IndexID:      deletedIndexID2,
+			IndexName:    "old_idx_2",
+			IsDeleted:    true,
+		}
+
+		segments := m.GetIndexedSegments(collID, []int64{segID}, []int64{fieldID})
+		assert.Len(t, segments, 1, "segment should be indexed even with deleted index entries")
+
+		// Cleanup
+		delete(m.indexes[collID], deletedIndexID1)
+		delete(m.indexes[collID], deletedIndexID2)
+	})
 }
 
 func TestMeta_MarkIndexAsDeleted(t *testing.T) {