diff --git a/src/Storages/MergeTree/MergeTreeData.cpp b/src/Storages/MergeTree/MergeTreeData.cpp
index 90c6b0784b4..c0ce0a2612a 100644
--- a/src/Storages/MergeTree/MergeTreeData.cpp
+++ b/src/Storages/MergeTree/MergeTreeData.cpp
@@ -4858,17 +4858,18 @@ void MergeTreeData::removePartContributionToColumnAndSecondaryIndexSizes(const D
         log_subtract(total_column_size.marks, part_column_size.marks, ".marks");
     }
 
-    auto indexes_descriptions = getInMemoryMetadataPtr()->secondary_indices;
-    for (const auto & index : indexes_descriptions)
+    for (auto & [secondary_index_name, total_secondary_index_size] : secondary_index_sizes)
     {
-        IndexSize & total_secondary_index_size = secondary_index_sizes[index.name];
-        IndexSize part_secondary_index_size = part->getSecondaryIndexSize(index.name);
+        if (!part->hasSecondaryIndex(secondary_index_name))
+            continue;
+
+        IndexSize part_secondary_index_size = part->getSecondaryIndexSize(secondary_index_name);
 
         auto log_subtract = [&](size_t & from, size_t value, const char * field)
         {
             if (value > from)
                 LOG_ERROR(log, "Possibly incorrect index size subtraction: {} - {} = {}, index: {}, field: {}",
-                    from, value, from - value, index.name, field);
+                    from, value, from - value, secondary_index_name, field);
 
             from -= value;
         };
diff --git a/tests/queries/0_stateless/02028_system_data_skipping_indices_size.reference b/tests/queries/0_stateless/02028_system_data_skipping_indices_size.reference
index e455643c01e..456f9d113be 100644
--- a/tests/queries/0_stateless/02028_system_data_skipping_indices_size.reference
+++ b/tests/queries/0_stateless/02028_system_data_skipping_indices_size.reference
@@ -1 +1,2 @@
 default	test_table	value_index	minmax	minmax	value	1	38	12	24
+default	test_table	value_index	minmax	minmax	value	1	38	12	24
diff --git a/tests/queries/0_stateless/02028_system_data_skipping_indices_size.sql b/tests/queries/0_stateless/02028_system_data_skipping_indices_size.sql
index 1efb9cff6a4..07237c43bea 100644
--- a/tests/queries/0_stateless/02028_system_data_skipping_indices_size.sql
+++ b/tests/queries/0_stateless/02028_system_data_skipping_indices_size.sql
@@ -12,4 +12,10 @@ ORDER BY key SETTINGS compress_marks=false;
 INSERT INTO test_table VALUES (0, 'Value');
 SELECT * FROM system.data_skipping_indices WHERE database = currentDatabase();
 
+ALTER TABLE test_table DROP INDEX value_index;
+ALTER TABLE test_table ADD INDEX value_index value TYPE minmax GRANULARITY 1;
+ALTER TABLE test_table MATERIALIZE INDEX value_index SETTINGS mutations_sync=1;
+
+SELECT * FROM system.data_skipping_indices WHERE database = currentDatabase();
+
 DROP TABLE test_table;