diff --git a/.changeset/fix-should-auto-remove-filter.md b/.changeset/fix-should-auto-remove-filter.md
new file mode 100644
index 0000000000..136bb1834b
--- /dev/null
+++ b/.changeset/fix-should-auto-remove-filter.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/table-core': patch
+---
+
+fix(table-core): respect custom `autoRemove` in `shouldAutoRemoveFilter`
diff --git a/packages/table-core/src/features/ColumnFiltering.ts b/packages/table-core/src/features/ColumnFiltering.ts
index 77b9927c04..6f93271b22 100644
--- a/packages/table-core/src/features/ColumnFiltering.ts
+++ b/packages/table-core/src/features/ColumnFiltering.ts
@@ -418,11 +418,9 @@ export function shouldAutoRemoveFilter<TData extends RowData>(
   value?: any,
   column?: Column<TData, unknown>,
 ) {
-  return (
-    (filterFn && filterFn.autoRemove
-      ? filterFn.autoRemove(value, column)
-      : false) ||
-    typeof value === 'undefined' ||
-    (typeof value === 'string' && !value)
-  )
+  if (filterFn?.autoRemove) {
+    return filterFn.autoRemove(value, column)
+  }
+
+  return typeof value === 'undefined' || (typeof value === 'string' && !value)
 }
diff --git a/packages/table-core/tests/shouldAutoRemoveFilter.test.ts b/packages/table-core/tests/shouldAutoRemoveFilter.test.ts
new file mode 100644
index 0000000000..5d6968c456
--- /dev/null
+++ b/packages/table-core/tests/shouldAutoRemoveFilter.test.ts
@@ -0,0 +1,73 @@
+import { describe, it, expect } from 'vitest'
+import { FilterFn } from '../src'
+import { shouldAutoRemoveFilter } from '../src/features/ColumnFiltering'
+
+const customAutoRemove: FilterFn<any> = (row, columnId, filterValue) => {
+  return filterValue === row.getValue(columnId)
+}
+customAutoRemove.autoRemove = (val) => val === undefined
+
+const neverAutoRemove: FilterFn<any> = (row, columnId, filterValue) => {
+  return filterValue === row.getValue(columnId)
+}
+neverAutoRemove.autoRemove = () => false
+
+const noAutoRemove: FilterFn<any> = (row, columnId, filterValue) => {
+  return filterValue === row.getValue(columnId)
+}
+
+describe('shouldAutoRemoveFilter', () => {
+  describe('with custom autoRemove defined', () => {
+    it('should use custom autoRemove result for empty string', () => {
+      expect(shouldAutoRemoveFilter(customAutoRemove, '')).toBe(false)
+    })
+
+    it('should use custom autoRemove result for undefined', () => {
+      expect(shouldAutoRemoveFilter(customAutoRemove, undefined)).toBe(true)
+    })
+
+    it('should use custom autoRemove result for null', () => {
+      expect(shouldAutoRemoveFilter(customAutoRemove, null)).toBe(false)
+    })
+
+    it('should use custom autoRemove result for zero', () => {
+      expect(shouldAutoRemoveFilter(customAutoRemove, 0)).toBe(false)
+    })
+
+    it('should use custom autoRemove result for false', () => {
+      expect(shouldAutoRemoveFilter(customAutoRemove, false)).toBe(false)
+    })
+
+    it('should keep undefined filter when custom autoRemove returns false for it', () => {
+      expect(shouldAutoRemoveFilter(neverAutoRemove, undefined)).toBe(false)
+    })
+  })
+
+  describe('without autoRemove defined', () => {
+    it('should remove undefined filter', () => {
+      expect(shouldAutoRemoveFilter(noAutoRemove, undefined)).toBe(true)
+    })
+
+    it('should remove empty string filter', () => {
+      expect(shouldAutoRemoveFilter(noAutoRemove, '')).toBe(true)
+    })
+
+    it('should keep null filter', () => {
+      expect(shouldAutoRemoveFilter(noAutoRemove, null)).toBe(false)
+    })
+  })
+
+  describe('without filterFn', () => {
+    it('should remove undefined filter', () => {
+      expect(shouldAutoRemoveFilter(undefined, undefined)).toBe(true)
+    })
+
+    it('should remove empty string filter', () => {
+      expect(shouldAutoRemoveFilter(undefined, '')).toBe(true)
+    })
+
+    it('should keep null filter', () => {
+      expect(shouldAutoRemoveFilter(undefined, null)).toBe(false)
+    })
+  })
+})