diff --git a/src/plugins/data/common/opensearch_query/opensearch_query/custom_filter_matches_index.test.ts b/src/plugins/data/common/opensearch_query/opensearch_query/custom_filter_matches_index.test.ts
new file mode 100644
index 000000000000..50a6084dafa6
--- /dev/null
+++ b/src/plugins/data/common/opensearch_query/opensearch_query/custom_filter_matches_index.test.ts
@@ -0,0 +1,51 @@
+/*
+ * Copyright OpenSearch Contributors
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { Filter } from '../filters';
+import { customFilterMatchesIndex } from './custom_filter_matches_index';
+import { IIndexPattern } from '../../index_patterns';
+
+describe('customFilterMatchesIndex', () => {
+  it('should return true if the custom filter has no meta', () => {
+    const filter = {} as Filter;
+    const indexPattern = { id: 'foo', fields: [{ name: 'bar' }] } as IIndexPattern;
+
+    expect(customFilterMatchesIndex(filter, indexPattern)).toBe(true);
+  });
+
+  it('should return true if no index pattern is passed', () => {
+    const filter = { meta: { index: 'foo', key: 'bar', type: 'custom' } } as Filter;
+
+    expect(customFilterMatchesIndex(filter, undefined)).toBe(true);
+  });
+
+  it('should return true if the custom filter has meta without a key', () => {
+    const filter = { meta: { index: 'foo', type: 'custom' } } as Filter;
+    const indexPattern = { id: 'foo', fields: [{ name: 'bar' }] } as IIndexPattern;
+
+    expect(customFilterMatchesIndex(filter, indexPattern)).toBe(true);
+  });
+
+  it('should return false if the filter is not custom', () => {
+    const filter = { meta: { index: 'foo', key: 'bar', type: 'match_all' } } as Filter;
+    const indexPattern = { id: 'foo', fields: [{ name: 'bar' }] } as IIndexPattern;
+
+    expect(customFilterMatchesIndex(filter, indexPattern)).toBe(false);
+  });
+
+  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(customFilterMatchesIndex(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(customFilterMatchesIndex(filter, indexPattern)).toBe(true);
+  });
+});
diff --git a/src/plugins/data/common/opensearch_query/opensearch_query/custom_filter_matches_index.ts b/src/plugins/data/common/opensearch_query/opensearch_query/custom_filter_matches_index.ts
new file mode 100644
index 000000000000..c98f6d1575a1
--- /dev/null
+++ b/src/plugins/data/common/opensearch_query/opensearch_query/custom_filter_matches_index.ts
@@ -0,0 +1,17 @@
+/*
+ * Copyright OpenSearch Contributors
+ * SPDX-License-Identifier: Apache-2.0
+ */
+
+import { IIndexPattern } from '../../index_patterns';
+import { Filter } from '../filters';
+
+export function customFilterMatchesIndex(filter: Filter, indexPattern?: IIndexPattern | null) {
+  if (!filter.meta?.key || !indexPattern) {
+    return true;
+  }
+  if (filter.meta?.type !== 'custom') {
+    return false;
+  }
+  return filter.meta.index === indexPattern.id;
+}
diff --git a/src/plugins/data/common/opensearch_query/opensearch_query/from_filters.ts b/src/plugins/data/common/opensearch_query/opensearch_query/from_filters.ts
index 990dca144abf..e7b13f5a10d6 100644
--- a/src/plugins/data/common/opensearch_query/opensearch_query/from_filters.ts
+++ b/src/plugins/data/common/opensearch_query/opensearch_query/from_filters.ts
@@ -34,6 +34,7 @@ import { filterMatchesIndex } from './filter_matches_index';
 import { Filter, cleanFilter, isFilterDisabled } from '../filters';
 import { IIndexPattern } from '../../index_patterns';
 import { handleNestedFilter } from './handle_nested_filter';
+import { customFilterMatchesIndex } from './custom_filter_matches_index';
 
 /**
  * Create a filter that can be reversed for filters with negate set
@@ -76,7 +77,10 @@ export const buildQueryFromFilters = (
     return filters
       .filter(filterNegate(negate))
       .filter(
-        (filter) => !ignoreFilterIfFieldNotInIndex || filterMatchesIndex(filter, indexPattern)
+        (filter) =>
+          !ignoreFilterIfFieldNotInIndex ||
+          filterMatchesIndex(filter, indexPattern) ||
+          customFilterMatchesIndex(filter, indexPattern)
       )
       .map((filter) => {
         return migrateFilter(filter, indexPattern);