diff --git a/.changeset/metal-papers-try.md b/.changeset/metal-papers-try.md
new file mode 100644
index 000000000..17383efd4
--- /dev/null
+++ b/.changeset/metal-papers-try.md
@@ -0,0 +1,5 @@
+---
+'@tanstack/offline-transactions': patch
+---
+
+Fix beforeRetry hook. When this hook filters out transactions during loadPendingTransactions(), those filtered transactions are removed from the outbox but remain in the scheduler. This causes them to be executed anyway, even though they were explicitly filtered out.
diff --git a/packages/offline-transactions/src/executor/TransactionExecutor.ts b/packages/offline-transactions/src/executor/TransactionExecutor.ts
index 441a87d88..f375c90bd 100644
--- a/packages/offline-transactions/src/executor/TransactionExecutor.ts
+++ b/packages/offline-transactions/src/executor/TransactionExecutor.ts
@@ -223,6 +223,9 @@ export class TransactionExecutor {
       filteredTransactions = this.config.beforeRetry(transactions)
     }
 
+    // Clear scheduler before reloading to ensure filtered-out transactions are removed
+    this.scheduler.clear()
+
     for (const transaction of filteredTransactions) {
       this.scheduler.schedule(transaction)
     }
diff --git a/packages/offline-transactions/tests/offline-e2e.test.ts b/packages/offline-transactions/tests/offline-e2e.test.ts
index b4f9442df..e800cdc3c 100644
--- a/packages/offline-transactions/tests/offline-e2e.test.ts
+++ b/packages/offline-transactions/tests/offline-e2e.test.ts
@@ -466,4 +466,111 @@ describe(`offline executor end-to-end`, () => {
 
     env.executor.dispose()
   })
+
+  it(`clears scheduler before reloading transactions with beforeRetry hook`, async () => {
+    // This test demonstrates the bug where filtered-out transactions
+    // remain in the scheduler after loadPendingTransactions is called
+    const storage = new FakeStorageAdapter()
+    let shouldFilterItem1 = false
+
+    // Create environment with a beforeRetry hook that can change behavior
+    const env = createTestOfflineEnvironment({
+      storage,
+      mutationFn: () => {
+        // Always fail to keep transactions in outbox
+        throw new Error(`offline`)
+      },
+      config: {
+        beforeRetry: (transactions) => {
+          if (shouldFilterItem1) {
+            // Filter out item-1 transaction, keep only item-2
+            return transactions.filter((tx) => tx.metadata?.item !== `item-1`)
+          }
+          return transactions
+        },
+      },
+    })
+
+    await env.waitForLeader()
+
+    // Create two transactions that will both fail
+    const tx1 = env.executor.createOfflineTransaction({
+      mutationFnName: env.mutationFnName,
+      autoCommit: false,
+      metadata: { item: `item-1` },
+    })
+    tx1.mutate(() => {
+      env.collection.insert({
+        id: `item-1`,
+        value: `first`,
+        completed: false,
+        updatedAt: new Date(),
+      })
+    })
+    tx1.commit()
+
+    const tx2 = env.executor.createOfflineTransaction({
+      mutationFnName: env.mutationFnName,
+      autoCommit: false,
+      metadata: { item: `item-2` },
+    })
+    tx2.mutate(() => {
+      env.collection.insert({
+        id: `item-2`,
+        value: `second`,
+        completed: false,
+        updatedAt: new Date(),
+      })
+    })
+    tx2.commit()
+
+    // Wait for transactions to be persisted to outbox
+    await waitUntil(async () => {
+      const entries = await env.executor.peekOutbox()
+      return entries.length === 2
+    })
+
+    // Verify both transactions attempted execution
+    await waitUntil(() => env.mutationCalls.length >= 2, 1000)
+    const initialCalls = env.mutationCalls.length
+
+    // Now lose leadership
+    env.leader.setLeader(false)
+    await flushMicrotasks()
+
+    // Enable filtering to filter out item-1 transaction
+    shouldFilterItem1 = true
+
+    // Regain leadership - this will call loadPendingTransactions
+    env.leader.setLeader(true)
+    await flushMicrotasks()
+
+    // Force immediate execution by notifying online
+    env.executor.notifyOnline()
+
+    // Wait for new execution attempts (should be much faster now)
+    await waitUntil(() => env.mutationCalls.length > initialCalls, 1000)
+
+    // Count executions after regaining leadership
+    const callsAfterReload = env.mutationCalls.slice(initialCalls)
+
+    // With the fix: Only item-2 transaction should be executed
+    // Without the fix: Both item-1 and item-2 would be executed
+    const item1Calls = callsAfterReload.filter(
+      (call) => call.transaction.metadata.item === `item-1`,
+    )
+    const item2Calls = callsAfterReload.filter(
+      (call) => call.transaction.metadata.item === `item-2`,
+    )
+
+    expect(item1Calls.length).toBe(0) // item-1 should NOT be executed
+    expect(item2Calls.length).toBeGreaterThan(0) // item-2 should be executed
+
+    // Verify only item-2 transaction remains in outbox
+    const finalOutbox = await env.executor.peekOutbox()
+    expect(finalOutbox.length).toBe(1)
+    expect(finalOutbox[0].metadata?.item).toBe(`item-2`)
+
+    env.executor.dispose()
+  })
 })