Payroll Liabilities incorrect after manually entering a missing payroll

Luicia2001 · ‎August 19, 2025

Hello,

In May, I had updated my Quickbooks version. After doing this, my last payroll disappeared. I know all employees were paid, but it was not showing in any records. Following the instructions found here, I reentered the missing payroll with a Direct Deposit offset and created a zero payroll. After doing that, my payroll liabilities were showing as unpaid in additional they were the wrong amount. I confirmed the original amount was paid to the IRS via EFTPS and bank statement. I adjusted the payroll liabilities for each employee, but that did not clear my payroll liabilities from showing as unpaid. How can I fix this?

Thank you in advance for any help.

Bryan_M · ‎August 19, 2025

I appreciate the detailed information you shared about the issue you encountered with your employees' payroll liabilities and the steps you performed to show the missing entries and offset them, @Luicia2001.

Since you confirmed that the reentered payroll liabilities are already paid via EFTPS and bank statement, and did not clear even by doing an adjustment, you can mark them as paid without affecting any of your payroll accounts by performing the backdoor process.

This action is performed to clear up historical tax payments, either current or previous years you entered, and avoid showing them in the bank register again to maintain your QuickBooks' correct balances. Here's how:

Go to the Help menu, pick About QuickBooks.
Press Ctrl + Alt + Y or Ctrl + Shift + Y to open the Setup YTD Amounts window.
Select Next until you reach the Enter prior payments section.
In the Enter Prior Payments segment, click Create Payment to see all prior tax and non-tax payroll liability payments you have made.
Enter the Payment Date and For Period Ending date accordingly based on the re-entered missing payroll to reflect them under Taxes and Liabilities.
Once they show up, hover your mouse over the Accounts Affected and choose Do not affect accounts to clear up balances without damaging your totals. Then, OK. If finished, tick Done. Then, Finish.

With regard to missing previous payroll after updating QuickBooks, if you have an assisted subscription, encountering this issue is possible if you did try restoring the file. To show them again, go to the Employees menu and Send Payroll Data.

It is also worth noting, you only need to select Send if the items showing in the field contains 0 paychecks for $0.00. If there are transactions listed, duplicate entries might occur. You'll want to contact payroll support to check what items have already been sent.

For additional assistance with clearing up your payroll liabilities balances, you can always return here. Have a good one.

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Payroll Liabilities incorrect after manually entering a missing payroll

Payroll Liabilities incorrect after manually entering a missing payroll

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