Troubleshooting Missing Tax Liabilities on an Additional Payroll

Overview

This article explains why tax liabilities may not appear or be paid after running an Additional Payroll, how to verify the payroll settings that generate liabilities, how to confirm whether payments were made through the system, and how to record manual payments when liabilities need to be paid outside the program. Use this guidance when an Additional Payroll has been processed but the associated tax liabilities do not appear in the ACH Transactions or Tax Payments areas.

How Additional Payrolls Should Behave

An Additional Payroll should generate tax liabilities and automatically adjust any pending tax deposit or compliance form. When liabilities are missing after an Additional Payroll, the most common causes are that the payroll was entered as a Prior Payroll (which does not generate tax forms) or that key payroll options were not set correctly before the data was entered. In some cases, all settings may appear correct and manual payment will be required to bring the client's account current.

Verification Checklist Before Assuming a System Issue

Before concluding that liabilities need to be paid manually, review the following settings to ensure the payroll was set up correctly to generate liabilities.

Confirm the Payroll Type

  • The payroll must be entered as Additional Payroll — not Prior Payroll. Prior Payroll does not generate tax forms.

  • Verify the payroll type shown in the payroll list matches the intended type.

Confirm the Pay Period and Pay Date

  • The Pay Period and Pay Date must be set in Payroll Options before entering any payroll data.

  • Changing dates after data has been entered may not update all downstream calculations correctly.

Confirm the Tax Method

  • Confirm the Tax Method is selected. For Additional Payrolls, taxes are calculated using the aggregate method.

  • If the tax method is missing or incorrect, taxes may not calculate as expected.

Confirm EFT Settings for Each Tax

  1. Select the Gear Icon.

  2. Navigate to E-Services > Taxes.

  3. For each tax item, verify the WHT/UI EFT box is checked.

  4. Confirm any required registration numbers or IDs are entered.

How to Confirm Whether Payments Were Made

If the settings above are correct and liabilities still do not appear, verify what has actually been recorded in the system before making any manual payments.

  1. In Payroll Relief, select E-Services from the left navigation.

  2. Select ACH Transactions and adjust the timeframe to review all electronic payments processed through the system.

  3. Navigate to Tax Payments > Payments Made to review payments recorded as paid through EFT or manual entry.

  4. Review the External tab under Tax Payments to see any external/manual payments that have been recorded.

  5. Compare the payments listed to the expected liabilities from the Additional Payroll to confirm whether any liabilities are truly missing.

How to Handle Missing Liabilities

If the settings are correct, the payroll was processed as an Additional Payroll, and liabilities are still missing after reviewing ACH Transactions, Payments Made, and the External tab, the taxes will need to be paid manually and then recorded in the system.

How to Pay and Record Manually

  1. Make the required tax payments directly to the appropriate tax agencies (for example, the IRS and applicable state agencies).

  2. In Payroll Relief, navigate to Tax Payments > External.

  3. Record each payment using the correct Tax Type, Period End Date, Date Paid, and Amount so the system reflects the payment history accurately.

  4. Confirm the recorded payments appear on the client's payroll and tax reports.

Verifying Tax Amounts Before Paying

Firms are responsible for verifying tax amounts before making payments on behalf of a client. Use the following in-system tools to confirm the amounts owed:

  • ACH Transactions to review electronic payments processed through the service.

  • Tax Payments > Payments Made to review EFT and recorded manual payments.

  • Tax Payments > External to review external/manual payments already recorded.

  • The payroll's tax liability report to identify the amounts generated for the specific Additional Payroll.

Tips for Preventing This Issue

  • Always set the Pay Period and Pay Date in Payroll Options before entering any payroll data.

  • Double-check the payroll type — Additional Payroll (not Prior Payroll) — before starting.

  • Confirm the Tax Method (aggregate for Additional Payrolls) is selected.

  • Verify EFT settings and registration IDs for each tax under the Gear Icon > E-Services > Taxes area at least once per client.

  • After each Additional Payroll, review ACH Transactions and Tax Payments > Payments Made to confirm liabilities were generated and scheduled.

Key Takeaways

  • Additional Payrolls should generate tax liabilities and adjust pending tax deposits or compliance forms automatically.

  • The most common causes of missing liabilities are entering the payroll as Prior Payroll instead of Additional Payroll, or setting the Pay Period, Pay Date, or Tax Method incorrectly.

  • Confirm payments through ACH Transactions, Tax Payments > Payments Made, and the External tab before assuming liabilities were missed.

  • If liabilities are genuinely missing, make the payments manually to the tax agencies and record them under Tax Payments > External.

  • Firms are responsible for verifying tax amounts before paying on the client's behalf.