It’s frustrating to open QuickBooks and find “Overdue Tax Payments” alerts even though you’ve already paid them. This common QuickBooks payroll issue not only causes confusion but also affects your reports and payment records. Many businesses face this QuickBooks tax problem after reconciling or updating payroll settings.

Fix QuickBooks showing overdue tax payments you already made. QuickBooks payroll issue help. Call +1-866-513-4656 for expert support.

If your QuickBooks continues to show overdue tax payments that were already submitted to the IRS or state agency, this article covers everything you need to know — from identifying causes to step-by-step solutions. You can also call QuickBooks Payroll Support at +1-866-513-4656 for personalized assistance from certified accounting experts

Why QuickBooks Shows Overdue Tax Payments Even After Payment

Several factors can cause QuickBooks to show overdue payroll or tax payments. Below are the most common reasons explained in detail.

1. Incorrect Payment Recording

You may have made the payment manually outside QuickBooks (e.g., through EFTPS or your state tax website) but not recorded it as “Paid” in QuickBooks. The system will still mark it as due unless it matches the internal record.

2. Payroll Tax Liability Not Updated

After paying taxes, QuickBooks updates the payroll liability account. If the update failed due to pending payroll data or incorrect check run, the tax may still appear as due in the liabilities.

3. Wrong Payment Period or Tax Agency Selected

When recording the payroll tax payment, using a wrong date range or selecting the wrong tax agency (Federal vs. State) can lead to discrepancies in your liability window.

4. Outdated Payroll Tax Table

Running QuickBooks without the latest payroll tax table may lead to QuickBooks error in tax tracking and reporting, displaying false overdue status.

5. Corrupted Data File or Sync Error

Sometimes, your QuickBooks data file (QBW) or payroll service connection can become corrupted, preventing updates from reflecting accurately.

Step-by-Step Solutions to Fix Overdue Tax Payment Issues

Follow these steps depending on whether you use QuickBooks Desktop or QuickBooks Online.

For QuickBooks Desktop

Step 1: Verify Your Payment Record

1. Go to Employees > Payroll Center.

2. Select the Pay Liabilities tab.

3. Check the Payment History section.

4. Find the tax payment and confirm the status (Paid/Unpaid).
   If your payment is not listed, proceed to record it manually.

Step 2: Record the Payment Manually

1. Click on Employees > Payroll Taxes and Liabilities > Create Custom Payments.

2. Choose the correct date range for the liability period.

3. Select the correct tax agency (e.g., IRS, State Department).

4. Mark the payment as already made and click Save & Close.

Step 3: Update Your Payroll Tax Table

1. Go to Employees > Get Payroll Updates.

2. Check Download Entire Update and click Update.

3. Once complete, restart QuickBooks.
   This ensures the latest tax rates and compliance forms are installed.

Step 4: Run the Verify and Rebuild Data Utility

1. Go to File > Utilities > Verify Data.

2. If errors are found, choose File > Utilities > Rebuild Data.

3. Follow the prompts to complete the repair process.

For QuickBooks Online

Step 1: Match the Payment

1. Click Taxes > Payroll Tax > Payments.

2. Locate your payroll tax payment.

3. If it shows “Overdue”, select Mark as Paid.

4. Enter the details of the payment (date, amount, confirmation number).

Step 2: Check Payroll Liability Account

1. Navigate to Settings  > Chart of Accounts.

2. Search for Payroll Liabilities.

3. Ensure the payment amount has been deducted correctly.

4. If not, adjust the transaction manually.

Step 3: Reconcile Your Bank Account

1. Go to Accounting > Reconcile.

2. Choose the bank account used for the tax payment.

3. Match payment transactions to your bank records to ensure proper sync.

Step 4: Update QuickBooks Payroll Settings

1. Go to Settings  > Payroll Settings > Tax Setup.

2. Review tax agency details (EIN, filing frequency, etc.).

3. Correct any outdated or mismatched information.

Prevention Tips 

To avoid seeing overdue tax payments in QuickBooks again:

• Always record manual tax payments immediately in QuickBooks.

• Keep your payroll tax table and software updated regularly.

• Reconcile your payroll liability accounts monthly.

• Double-check the agency and date range before submitting payments.

• Backup your company file weekly to prevent data corruption.

When to Contact Support

If the overdue issue persists after following these steps, the problem may be linked to deeper data or payroll configuration errors. Don’t risk incorrect filings — contact QuickBooks Payroll Support at +1-866-513-4656 for professional help restoring your account accuracy and compliance.

FAQs

1. Why does QuickBooks still show taxes as overdue after paying them?
This usually happens when the tax payment is made outside QuickBooks or isn’t recorded properly within the payroll system.

2. Will the overdue notice affect my payroll filings?
No, as long as you’ve paid the tax. However, leaving the record unreconciled can cause reporting discrepancies.

3. How can I verify that QuickBooks updated my payroll tax payment?
Use the Payroll Center > Payment History (Desktop) or Taxes > Payments (Online) to confirm the payment recorded date and amount.

4. Can a tax table update fix this QuickBooks error?
Yes. Installing the latest payroll tax table often corrects tracking issues and overdue notices.

5. Should I call QuickBooks support for payroll tax problems?
Yes. If you notice incorrect liability balances or recurring overdue alerts, call support at +1-866-513-4656 for personalized assistance.