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Understanding taxes you already paid when you set up QuickBooks Online Payroll

Learn about the “Which tax payments you have made this quarter” window.

When you set up QuickBooks Online Payroll, you confirm what taxes you paid already. Sometimes this can be a little tricky, so here are some answers to frequently asked questions to help finish your payroll setup.

What is the “Which tax payments have you made this quarter” window?

This window summarizes the tax amounts that are due based on previous entries you made earlier during the employee and tax setup process. You’ll see all your payroll tax liabilities for the current quarter. QuickBooks calculated these amounts based on the current year payroll and state tax rate info you entered.

Why does QuickBooks need this info?

Knowing which payroll liabilities are owed and paid will help us pick up where you left off before using QuickBooks.

QuickBooks will use this info to ensure accurate paycheck calculations, and assist you with future tax payments and form filings.

Incorrect amounts may result in under or overpaid tax payments, duplicate tax payments, tax notices with fines and penalties.

Note: If taxes are overpaid to the government, you will be responsible for requesting an overpayment refund, if possible.

Where do these numbers come from?

If you paid employees this year, during the setup process you entered prior paycheck totals for each employee and prior paycheck company totals for each payroll date. It's important to fill these amounts carefully so we know what taxes you're still liable for, and which we might need to file and pay on your behalf.

Compare the amounts you entered in QuickBooks to reports and federal and state tax form filings from your prior payroll provider that reflect total employee and employer taxes calculated and paid for each quarter. For more information about types of reports to use, see Learn about reports to use to enter prior payroll.

  1. Go to Payroll, then the Employees tab.
  2. Select the employee, then scroll to Step 8 and select Edit ✏️.
  3. Make the necessary adjustments then select Continue.

Note: Some payroll services impound taxes, meaning they debit your bank account for all employee and employer taxes at the time you run payroll. When you cancel service in the middle of a quarter, those services may refund any unpaid taxes they’ve already collected. If you aren’t sure what taxes have been paid or will be refunded, contact your prior payroll provider.

What if the amounts don't match what I paid?

When setting up your payroll account, you may enter payrolls and tax payments from earlier in the year that were processed by another service. That service may have used slightly different calculations that cause small differences from what QuickBooks expects. If all of the info you've entered are correct, contact us for assistance with these discrepancies.

Review the prior payroll pay history entered for each employee and ensure each number matches exactly to the reports from your prior payroll provider. Correcting the pay history entered will correct the calculation of company tax payments due.

  1. Go to Payroll, then the Employees tab.
  2. Select the employee, then scroll to Step 8 and select Edit ✏️.
  3. Make the necessary adjustments then select Continue.
  1. Go to the Overview page, then select Step 3 again.
  2. Select Continue until you get to the State tax details screen.
  3. Adjust the rates as needed then select Continue then Done.
If you made any partial payments, don’t mark them as paid, contact us for the next steps.
Tax penalties are not part of the amount due for payroll taxes, and are not reported on any filings. When entering prior tax amounts paid during payroll setup, exclude any amounts paid for penalties or interest.

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