QBO overpaid Federal and State withholding.

Ani3 · ‎March 13, 2026

I switched my client to QBO payroll for the 1/30/26 payroll. I entered everything for the previous payrolls that were run on 1/2 and 1/16. I marked that these payments had already been made. Regardless, Quickbooks withdrew from the bank account an amount equivalent to the prior periods Federal and State withholding. That amount was then sent to the taxing agencies. The payments from Quickbooks were netted together for the 1/2 and 1/16 payroll and was made on 2/17/26.

I called Quickbooks support and after an hour and 45 minutes the best answer was to call the taxing agencies.

Here is the problem, Quickbooks does not show that the original payments were made so the Federal 941 and 943 are going to be wrong as well as the State withholding reports.

Do I wait until the quarterlies are filed and then file an amendment? Can I file that thorugh QBO?

What are my best options? Thanks in advance.

EvethC · ‎March 13, 2026

Hi there, Ani. Filing amendments through QuickBooks Online (QBO) for Federal 941 and 943 is unavailable. If the quarter hasn't ended yet, you can leave the overpayment as is. QuickBooks will automatically apply that credit to any new payroll taxes you owe during the rest of the quarter. Whatever's left over when the quarter closes will show up as an overpayment on your tax return.

To resolve this, here's what to do:

Go to All apps, then Payroll, then Payroll taxes.
Select Payments.
Find the overpaid tax, then select Resolve.
Choose either Request a refund or Apply to a future tax payment.
Select Confirm, then Done.

It is best to request a refund only if the quarter where the credit was generated has closed. If your auto-pay and file feature is active, QuickBooks will select the refund option for you during filing to keep your records balanced. Also, you should only choose to apply the credit to a future tax payment if you have verified that the credit is valid and has not already been used for another tax liability.

Please note that you'll still need to contact the IRS or your state tax agency separately to request a refund or confirm that the credit will be applied to a future period.

You can respond by tapping the reply button for further clarification and information regarding your tax overpayments. We'd be here to assist you!

EvethC

Good day, Ani.

I just wanted to follow up to check if the assistance I provided helped address your concern.

We’ll be glad to assist further if needed.

Topics

Training

Community

Resources

QBO overpaid Federal and State withholding.

QBO overpaid Federal and State withholding.

QBO overpaid Federal and State withholding.

Need to get in touch?