941 Schedule B liability line item doesn't match payroll summary

Thanks for posting to the Community, @jennrobe.

Let me share some insights on how to view the 941 Schedule B liability line item.

QuickBooks is adding the tax liability showing on Schedule B for the total taxes accrued each day on paychecks for Federal Withholding, Medicare Employee, Medicare Company, Social Security Employee, and Social Security Company. It doesn't suppose to differ the COVID 19 credit.

You can run the Payroll Summary report and customize it to show the Payroll item for Federal Withholding, Medicare Company, Medicare Employee, Social Security Company, and Social Security Employee to show the amounts in Schedule B (Line 16).

Here's how:

1. Go to Reports, select Employees & Payroll, then select Payroll Summary.
2. Select Customize Report, then select the Display tab.
3. Select Last Calendar Quarter from the Dates dropdown list.
4. In the Display columns by dropdown list, select Month, then clear the Hours and Rate checkboxes.
5. Select the Filters tab.
6. Choose the Payroll Item in the Filter dropdown list, and then choose Selected payroll items in the Payroll Items dropdown list.
7. In the Payroll Item window, select Federal Withholding, Medicare Company, Medicare Employee, Social Security Company, and Social Security Employee. Clear any other selected items, then select OK.
8. Select OK to return to the Payroll Summary report.
9. Ignoring any negative signs, add up each column's amounts for Federal Withholding, Medicare Company, Medicare Employee, Social Security Company, and Social Security Employee taxes. The totals should correspond to the amounts in Month 1, Month 2, Month 3, and "Total liability for quarter" of line 16.
10. You can double-click any of the numbers on the report to see what transactions contribute to their amounts.

The bulk of the COVID wages you paid for from the first to third month should total the amounts in Line 13e.

This way, I'd suggest consulting a tax accountant to help you with the amounts.

I'll be adding this article as your source to know more details about how QuickBooks populates the lines on Form 941: How QuickBooks Populates The 941. It includes links on how QuickBooks fill the other forms.

Feel free to ask questions below if you need clarifications. I'll keep my notifications open. Take care!