diff --git a/.changeset/wet-hairs-lick.md b/.changeset/wet-hairs-lick.md
new file mode 100644
index 0000000..eff4301
--- /dev/null
+++ b/.changeset/wet-hairs-lick.md
@@ -0,0 +1,7 @@
+---
+'@tanstack/store': patch
+---
+
+Fix a regression where mutable atoms could be updated internally with no updater and have their snapshot replaced with `undefined`.
+
+Mutable atoms now ignore internal no-argument `_update()` calls, while computed atoms keep existing recomputation behavior. This prevents external-store state from disappearing during reactive graph cleanup.
diff --git a/packages/store/src/atom.ts b/packages/store/src/atom.ts
index 1aadc08..624c35b 100644
--- a/packages/store/src/atom.ts
+++ b/packages/store/src/atom.ts
@@ -176,9 +176,15 @@ export function createAtom<T>(
     _update(getValue?: T | ((snapshot: T) => T)): boolean {
       const prevSub = activeSub
       const compare = options?.compare ?? Object.is
-      activeSub = atom
-      ++cycle
-      atom.depsTail = undefined
+      if (isComputed) {
+        activeSub = atom
+        ++cycle
+        atom.depsTail = undefined
+      } else if (getValue === undefined) {
+        // Mutable atoms can be marked dirty by the reactive graph, but they should
+        // never be recomputed without an explicit value/updater.
+        return false
+      }
       if (isComputed) {
         atom.flags = ReactiveFlags.Mutable | ReactiveFlags.RecursedCheck
       }
diff --git a/packages/store/tests/store.test.ts b/packages/store/tests/store.test.ts
index 0c2903f..ab8d47b 100644
--- a/packages/store/tests/store.test.ts
+++ b/packages/store/tests/store.test.ts
@@ -67,4 +67,12 @@ describe('store', () => {
     store.setState(() => 24)
     expect(fn).toBeCalledWith({ prevVal: 12, currentVal: 24 })
   })
+
+  test('mutable store should ignore internal no-arg updates', () => {
+    const store = createStore({ pageIndex: 1 })
+    const atom = (store as any).atom
+
+    expect(atom._update()).toBe(false)
+    expect(store.state).toEqual({ pageIndex: 1 })
+  })
 })