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Fix underpaid payroll taxes

by Intuit•11• Updated 6 days ago

Learn how to handle underpaid taxes in QuickBooks Payroll.

Did you receive a notice from the IRS or state agency that you owe additional money for some taxes? Or do you see an amount due in QuickBooks for taxes you thought you already paid? 

Here’s some reasons you may owe additional taxes:

  • A tax rate increased
  • You created additional paychecks for a period in which you already paid taxes
  • You requested a payroll correction that created additional taxes due 

Here’s how to fix the underpayment.

You received a tax notice from the IRS or state

Send us your notice and we can help you take care of the underpayment.

You see an additional amount due in QuickBooks

Fixing the underpaid tax depends on the tax you’re dealing with. Select the tax you need to fix, then select your payroll plan

Note: Not sure which payroll service you have? Here's how to find your payroll service.

Federal taxes (Social Security, Medicare, Federal Income Tax) or State Income Tax (SIT)

We’ll pay the additional amount owed for you.

  1. Select Taxes, and then Payroll Tax.
  2. Select Payments.
  3. Select one of the following:
    • Pay (if available): this will send the payment electronically
    • Mark as paid: this will record the payment if you made it outside the system
  4. Follow the on-screen instructions once you select one of the options.

Contact us for help with your tax underpayment.

If you're set up to e-pay in QuickBooks, you can e-pay the additional amount due.

Or you can send the payment directly to the agency. You’ll need to record the tax payment in QuickBooks. 

State Unemployment Insurance (SUI)

We can only make one SUI tax payment per quarter for you. You’ll need to pay the amount due directly to the agency, then record the payment in QuickBooks.

  1. Go to Payroll, then select Overview.
  2. Look for a task to make the additional payment directly to your state unemployment agency.
  3. Select Taxes, and then Payroll Tax.
  4. Select Payments.
  5. Select Mark as paid.
  6. Select one of the following:
    • No, record manually if you need to add the payment to your QuickBooks ledger.
    • Yes, mark paid if you don’t need to add the payment to your QuickBooks ledger.
  7. Follow the on-screen instructions once you select one of the options.

You can only make one SUI tax payment per quarter in QuickBooks. You’ll need to pay the amount due directly to the agency, then record the payment in QuickBooks.

  1. Select Taxes, and then Payroll Tax.
  2. Select Payments.
  3. Select Mark as paid.
  4. Select one of the following:
    • No, record manually if you need to add the payment to your QuickBooks ledger.
    • Yes, mark paid if you don’t need to add the payment to your QuickBooks ledger.
  5. Follow the on-screen instructions once you select one of the options.

Contact us for help with your tax underpayment.

If your tax rate increased, here's how to correct the calculation and payments. 

  1. Update your SUI rate.
  2. Run a payroll check up for QuickBooks to correct past paychecks.
  3. Review a payroll summary report to make sure your SUI amounts are correct.
  4. Send the additional amount due directly to the SUI tax agency. You can only make one SUI payment per quarter in QuickBooks. Contact your state if you need assistance paying the additional tax due.
  5. Record the payment in QuickBooks Desktop.
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