diff --git a/src/plugins/data/common/opensearch_query/opensearch_query/filter_matches_index.test.ts b/src/plugins/data/common/opensearch_query/opensearch_query/filter_matches_index.test.ts
index f610b1e7179..ad68e14b2c5 100644
--- a/src/plugins/data/common/opensearch_query/opensearch_query/filter_matches_index.test.ts
+++ b/src/plugins/data/common/opensearch_query/opensearch_query/filter_matches_index.test.ts
@@ -66,4 +66,18 @@ describe('filterMatchesIndex', () => {
 
     expect(filterMatchesIndex(filter, indexPattern)).toBe(true);
   });
+
+  it('should return false if the custom filter is a different index id', () => {
+    const filter = { meta: { index: 'foo', key: 'bar', type: 'custom' } } as Filter;
+    const indexPattern = { id: 'bar', fields: [{ name: 'foo' }] } as IIndexPattern;
+
+    expect(filterMatchesIndex(filter, indexPattern)).toBe(false);
+  });
+
+  it('should return true if the custom filter is the same index id', () => {
+    const filter = { meta: { index: 'foo', key: 'bar', type: 'custom' } } as Filter;
+    const indexPattern = { id: 'foo', fields: [{ name: 'barf' }] } as IIndexPattern;
+
+    expect(filterMatchesIndex(filter, indexPattern)).toBe(true);
+  });
 });
diff --git a/src/plugins/data/common/opensearch_query/opensearch_query/filter_matches_index.ts b/src/plugins/data/common/opensearch_query/opensearch_query/filter_matches_index.ts
index f8c2ab67ee9..529e68609ae 100644
--- a/src/plugins/data/common/opensearch_query/opensearch_query/filter_matches_index.ts
+++ b/src/plugins/data/common/opensearch_query/opensearch_query/filter_matches_index.ts
@@ -31,14 +31,14 @@
 import { IIndexPattern, IFieldType } from '../../index_patterns';
 import { Filter } from '../filters';
 
-/*
- * TODO: We should base this on something better than `filter.meta.key`. We should probably modify
- * this to check if `filter.meta.index` matches `indexPattern.id` instead, but that's a breaking
- * change.
- */
 export function filterMatchesIndex(filter: Filter, indexPattern?: IIndexPattern | null) {
   if (!filter.meta?.key || !indexPattern) {
     return true;
   }
+
+  if (filter.meta?.type === 'custom') {
+    return filter.meta.index === indexPattern.id;
+  }
+
   return indexPattern.fields.some((field: IFieldType) => field.name === filter.meta.key);
 }