How to fix common Payroll errors in QuickBooks

How to fix common Payroll errors in QuickBooks

Payroll tax returns have been prepared and filed showing no balance due (and no notices to the contrary have been received) Payroll, (and inventory discussed elsewhere), are two areas where QuickBooks® is less forgiving and clients are more likely to make mistakes. Most often the errors are the result of incorrect or inconsistent procedures.

The most common error in this area is that the Pay Payroll Liabilities feature was not used; rather payroll tax payments were entered using Write Checks or Enter/Pay Bill functions.

Common Error: Clients Write Checks (or use check register) to pay payroll tax liabilities.


  • Payroll Liabilities are higher than expected
  • Payroll Tax Expense is higher than expected
  • Bank account balance appears correct

Warnings Reduce Errors

QuickBooks does warn users in several instances when the recommended procedures are not followed. If users heed the warnings, errors are often avoided. However, some users will click past these warnings and still process the payroll incorrectly perhaps for a lack of understanding as to how to do otherwise.

A client must first subscribe to one of Intuit’s payroll offerings for payroll to be established. Once payroll is installed, a Payroll Setup Tool walks the client through the process.

QuickBooks payroll works best when all payroll activity is performed from within the payroll menus. This includes paying accrued payroll taxes to the respective taxing authorities. If the company has written checks or used the Enter/Pay Bills entered bills functionality to pay for these liabilities, and the QuickBooks-created Payroll Liabilities account was assigned, the following warning message appears:

This message warns but does not prevent users about using the wrong type of payment (i.e., Write Checks or Enter/Pay Bills) when attempting to make payroll liability payments. When the user clicks the Pay Payroll Liabilities button in the warning message, the user is directed to the Select Date Range for Liabilities dialog. The message directs the user to use the Pay Payroll Liabilities feature to create a payroll liability check.

Find Incorrectly Paid Payroll Liabilities

In the Client Date Review, the Find Incorrectly Paid Payroll Liabilities tool, generates a report of all the manual check transactions coded to a Payroll Tax vendor. The entries made outside of the Pay Scheduled Liabilities function in the Payroll Center are displayed.

Correcting Payroll Liability Payment Errors

Payroll tax liability payments can be corrected via two methods. First, if a check or bill payment was used to pay a payroll liability, determine if the check or bill payment check has been cleared in a bank reconciliation. If not, void the existing check or bill that is paying the payroll liabilities and recreate the check correctly by selecting Employees > Payroll Taxes & Liabilities, then Pay Scheduled Liabilities.

The second method should be used if the check or bill payment check was used and that check has been cleared in a bank reconciliation. If the check or bill payment check is voided, the bank reconciliation with be affected. Using a Journal Entry is never a preferred method to make the correction, instead the Payroll Liability Adjustment option should be used to make the correction.

Getting the Red Out – Clearing Out Past Due Liabilities

The Pay Scheduled Liabilities section in the Payroll Center may have red overdue amounts showing when none exist. The liabilities amounts appear in the section when a payroll is generated and are only reduced when the Pay Scheduled Liabilities method is used to pay the taxes due. If the liabilities were recorded through any other method, such as a check being written and coded to the Payroll Liabilities account, the liabilities shown as due will not be reduced.

1. First, verify that the liabilities have been paid.

2. Select the appropriate item from the Pay Scheduled Liabilities window as shown below and click the View/Pay button.

3. In the Liability Payment – Checking window, change the check amount to zero.

4. Add additional lines in the expenses area for the same accounts already listed with a negative amount to offset the entry.

5. Include the check number actually used to pay the liabilities in the memo section as a reference.

6. The result will be offsetting amounts to the liabilities accounts which will clear the Pay Scheduled Liabilities window, but not affect the general ledger accounts.

Additional Areas to Troubleshoot Payroll Errors

Importance of Payroll Item Account Mapping

Payroll items must be assigned an account so payroll transactions can be properly recorded in the general ledger. Errors in the set up of the payroll item mapping can be located through a Payroll Items Listing report. Select Reports > Lists > Payroll Item Listing report. This report shows the payroll earnings, deductions, and tax items as well as the current tax table limits and rates. Use this report to ensure the desired General Ledger account is being used. Double-click on any item to make changes. Changes can be applied to all transactions, future and prior, only prior transactions from a date forward or no prior transactions.

Reconciling Payroll Transactions in the Bank Reconciliation Process

The Intuit payroll subscription will determine whether all federal and state payroll tax forms for filing are available within QuickBooks. If you or the client is preparing the payroll, it is wise to first complete the bank reconciliation to determine any payroll liability payments which have not cleared and handle them accordingly.

Locating Non-Payroll Transactions

Users sometimes override error message and record transactions that should appear on payroll reports. Identifying these before the payroll tax returns are prepared and filed can save the time to amend or correct these payroll returns later on.

From the Employees menu, choose Employee Center, then the Transactions tab. From this area, select the Non-Payroll Transactions and in the Date area, select the time period for which the payroll reports are being generated.

Shown in the example below is a non-payroll check issued to Gregg. While the check may be recorded properly, this check may also be recorded improperly. This review will make that determination.

Creating Payroll Liability Checks Directly in the Checkbook Register

To properly process payroll liability checks, select Employees > Employee Center > Payroll tab, then View/Pay Scheduled Liabilities. Payroll Liability checks should be generated from this section. However, checks are often created directly from the register or via Write Checks. The Pay Scheduled Liabilities section in the Payroll Center is then incorrect. See the Getting the Red Out—Clearing out Past Due Liabilities section earlier for step by step instructions on how to correct these entries.

If the liabilities need to be adjusted and the bank account has been reconciled in QuickBooks, another way to correct the liability is by selecting Employees > Employee Center > Payroll tab and choose Related Payment Activities > Adjust Payroll Liabilities. The Liability Adjustment window appears and changes can be made either to or not to affect the General Ledger accounts depending on how the checks to pay the liabilities were originally written.

NOTE: Choose Do not affect accounts if the General Ledger is correct overall and should not be affected. This situation would arise if the client paid the correct amount of the payroll liability and used the correct General Ledger coding on the checks written to the taxing authorities, but simply did not write the checks correctly using the Pay Scheduled Liabilities area of QuickBooks.

In the example shown above, we are choosing to affect the Liability and Expense Accounts. The following dialog box appears. The general ledger will be update with the adjustment.