QB Issue Resolution:

The bonus checks need to be run through payroll. Did you pay them through the “Write Checks” function? If so, to fix this you will need to run a payroll paying those employees. You will use the same check numbers as the original checks were. Once you have created the checks through payroll you will go back and void the original checks.

You will need to increase the gross amount so the net amount is what you actually paid the employee. Depending on what payroll subscription you have (if any) will determine how you do this. When creating the payroll check, open the check details. Look at the bottom right hand corner to see if “Enter Net/Calculate Gross” is available for you to check. If so, then check it and enter the net amount of the check. QuickBooks will calculate the Gross for you. If not, you will need to manually calculate what the gross should be and enter that. You may have to adjust either the Federal or State taxes by a few cents to get the exact net you paid. Do not adjust Social Security or Medicare. Make sure these new checks are for the EXACT net amount as the originals. Once this is done don’t forget to void the original checks.

Resolution for Issue 'Bonus checks not run through payroll.' available: Yes (Solved).
Source: Intuit Community forum.

Bonus checks not run through payroll.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

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