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Set up QuickBooks Online Payroll to pay and file your payroll taxes and forms

by Intuit•167• Updated 1 month ago

Learn about options to pay and file your 941, 944, 943, state, and local taxes using QuickBooks.

You have the flexibility to choose how you want your payroll taxes and filings handled. Select your option below to see the tasks you'll need to complete. 

Important: Once Auto-Pay/File is enabled, on the 1st of the following month, it will start automatically processing any tax payments moving forward. If you have any tax liabilities from a period prior to when Auto-Pay/File is ENABLED, you will still be responsible for manually processing those before the Tax Filing System takes over the future payments.

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Take care of your tax payments and filings automatically or electronically

Complete these tasks so QuickBooks will pay your taxes and file your forms automatically, or you can do them electronically in QuickBooks.

Note: If you have QuickBooks Online Payroll Core, local taxes aren't automated. To automate those payments and filings, you'll need to upgrade to QuickBooks Online Payroll Premium or Elite.

Step 1: Check or change your taxes and forms preference

  1. Go to Settings ⚙, then select Payroll Settings.
  2. From the Taxes and forms section, select Edit ✎.
  3. Review or choose one of the following:
    • If you want QuickBooks to automatically pay your taxes and file your forms, select Automate taxes and forms.
    • If you want to pay and file electronically in QuickBooks, select I’ll initiate payments and filings using QuickBooks.
  4. Select Save, then Done. 

Step 2: Check the automate taxes widget for tasks you need to complete

The Automate taxes widget gives you detailed info about each tax. 

  1. Go to Payroll, then select Overview.
  2. From Automate taxes, select Finish up. 
  3. Review the Status and Who pays & files column for each tax. 
  4. If there are warnings in the status, select the Action link (Finish up, Start, Mark as done). 

Note: if you’re viewing this article from Help in your QuickBooks, you’ll need to close it to see the Action column. 

  1. Complete the task(s) as needed.  If you need additional help with a particular task, see the list of tasks below. 

Tax setup tasks

Select the task below that you need help with.

If you didn’t connect your bank during the initial payroll setup, you’ll need the following info:

  • Legal business name, address, and phone number
  • Principal officer name, address, date of birth, mobile phone number, and Social Security number
  • Bank account to use for tax payments and direct deposit - either your Online bank login credentials to connect instantly, or the routing and account number if you need to connect manually.

If you weren’t able to connect instantly: 

  1. Check your payroll bank account for a deposit of less than 1.00 from QuickBooks Payroll. 
  2. Select Edit ✎ on the Watch your bank account for a small deposit task, and enter the amount. 

On this task you’ll need to enter any missing info:

  • Account number or FEIN
  • How often you pay your taxes (deposit frequency)
  • Rate(s)

If you don’t have, or can’t find your state tax info, see Access state agency websites. Then you can register, look up your info, or contact the state agency. 

For local tax agency info:

If your business isn’t subject to a tax (doesn’t need to pay or report wages), leave the account number blank and enter or select 0 for the rate. 

Some states require you to authorize us as your third party administrator to pay and file on your behalf. You’ll do this on your state’s website. Select your state below for instructions:

Your Principal Officer needs to complete this task. They’ll be asked specific questions that only they can answer/verify. 

Pay and file your taxes and filings yourself

Complete these tasks so QuickBooks can accurately track your tax amounts and populate the 941, 944, 943, state, and local tax forms.  You can generate the payments and filings in QuickBooks to send to the agencies. 

Step 1: Check or change your taxes and forms preference

  1. Go to Settings ⚙, then select Payroll Settings.
  2. From the Taxes and forms section, select Edit ✎.
  3. If you want to handle your taxes and filings yourself, select I’ll pay and file the right agencies through their website or by mail.
  4. Select Save, then Done. 

Step 2: Complete your tax setup

Set up federal (941, 944, 943), state, or local taxes

On this task, be sure to enter your tax rates.  

If you want to print any tax forms from QuickBooks to send to the agencies, we recommend adding your account numbers and how often you pay your taxes. 

If you don’t have, or can’t find your state tax info, see Access state agency websites. Then you can register, look up your info, or contact the state agency. 

For local tax agency info:

If your business isn’t subject to a tax (doesn’t need to pay or report wages), leave the account number blank and enter or select 0 for the rate. 

QuickBooks Online Payroll CoreQuickBooks Online Payroll EliteQuickBooks Online Payroll Premium

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