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Level 3

Can QuickBooks file and pay quarterly taxes every payroll (biweekly)?

We would like to pay taxes every payroll (2 weeks), instead of quarterly.


Is it possible to setup QuickBooks to pay payroll taxes every 2 weeks? (instead of quarterly)?


If yes, can this be setup as scheduled recurring payment?



7 Comments 7

Can QuickBooks file and pay quarterly taxes every payroll (biweekly)?

Hi DesktopPayroll2021!


Thank you for always visiting us here in the QuickBooks Community!


It's great news for you because you can schedule a tax payment on every payroll. I'll be happy to walk you through the setup.


  1. Go to Employees and choose Payroll Center.
  2. Click the Pay Liabilities tab on the right page.
  3. In the Other Liabilities section, click on Change Payment Method.
  4. In the QuickBooks Payroll Setup window, select Schedule payments.
  5. Click the tax that you want to create a schedule for and select the Edit button.
  6. Choose a payment (deposit) method, whether Check or E-pay, and select your tax agency.
  7. In the Payment (deposit) frequency drop-down menu, choose After each payroll (Semiweekly). You can also put a check on Let me use a different payment (deposit) frequency and click Next.
  8. On the next page, set the number of days after the paycheck date you pay your tax liability and click Finish.


You can also check about setting up and paying scheduled or custom (unscheduled) liabilities for your additional reference.


Please don't hesitate to reach back out if you have questions along the way. The QuickBooks Team is always here to assist you.

Level 3

Can QuickBooks file and pay quarterly taxes every payroll (biweekly)?

Thank you. I'll be trying your suggested setup ASAP.


Which taxes are we able to pay biweekly?

QuickBooks Team

Can QuickBooks file and pay quarterly taxes every payroll (biweekly)?

I appreciate you for getting back, @DesktopPayroll2021. Let me share with you some additional information about filing and paying taxes in QuickBooks Desktop (QBDT).


The system is dependent on the filing requirements or schedule set by the state or IRS. The schedule of filing and paying from one state or agency to another may vary. For now, you can select the links for your state to find details on tax forms, withholdings, unemployment, and other tax, e-file and pay information, general state, and agency information, and employer registration from here: Payroll Tax Compliance Links.


If you need to change the frequency of your quarterly taxes to biweekly, you may prepare your liabilities outside QuickBooks or reach out to your agency for options in this scenario. 


On the other hand, you can learn more about managing liability and pay schedules from these articles:



If you have any other follow-up questions about payroll or tax filings, let me know by adding a comment below. I'm always here to help. Have a good one!

Level 1

Can QuickBooks file and pay quarterly taxes every payroll (biweekly)?

This was exactly the question and answer I've been looking for. However, the interface of the screenshots and directions you provided seems to have changed. Can you answer this exact questions again, but with updated directions and screenshots?

QuickBooks Team

Can QuickBooks file and pay quarterly taxes every payroll (biweekly)?

We appreciate you joining the thread, @kaceybat. We'll provide the details you need to file and pay quarterly taxes in a bi-weekly setup inside QuickBooks Online (QBO) Payroll.


Before digging deeper into your query, know that the steps and screenshots provided in this thread are for QuickBooks Desktop (QBDT) Payroll users. Thus, it's why the interface looks different from QBO.


To get through this and get you ready for a bi-weekly schedule. We'll write down the steps to get you going:


  1. Access your QuickBooks Online company.
  2. On the left navigational bar, go to the Payroll tab.
  3. Select Employees.
  4. Go to the Employee details section and click Edit.
  5. In the Pay schedule field, select + Add pay schedule.
  6. In the Pay frequency field, choose Every other week.
  7. Fill out the appropriate fields. Then select Save.
  8. Once everything is good, click the Save button to keep the changes.


Feel free to visit this page for more details: Set up and manage payroll schedules.


On the other hand, we got these articles to help you keep track of your payroll activities and ensure all data entered inside the program remains accurate:



It'll always be our pleasure to have you here again if you need help managing the payroll schedule inside the program. We're always ready to provide further assistance to address all your queries. Have a good one.

Level 1

Can QuickBooks file and pay quarterly taxes every payroll (biweekly)?

Thanks I've got the payroll schedule set up to run every other week, however I noticed that taxes were not automatically taken at the time of payroll. I'm thinking because I'm using the most basic form of QBO, I'm not able to schedule taxes to actually be paid every other week and that I'll need to wait until the automatic payments are made on the quarterly basis, is that correct?

QuickBooks Team

Can QuickBooks file and pay quarterly taxes every payroll (biweekly)?

It's good to know you successfully set up your payroll schedules in QuickBooks Online Payroll (QBOP), kaceybat


Since you noticed the taxes weren't automatically deducted during payroll, you should check to see if your employee is tax-exempt by going to the Payroll menu. It's also advisable to check the Payroll Settings.  


Here's how: 


Step 1: Check in the Payroll menu. 


  1. Go to the Payroll menu located at the left navigation panel and choose the Employees option. 
  2. Select an employee. 
  3. Find the Tax withholding section and click Edit
  4. Scroll down until you see the Tax exemptions dropdown. You'll see if your employee has one of those tax exemptions. 
  5. If you made some changes, click Save once done. Otherwise, press the Exit button. 


Step 2: Check in the Payroll Settings.


  1. Go to the Gear icon located in the upper left corner.
  2. Under the Your Company column, select Payroll Settings
  3. Scroll down until you see the Employee Profile Management section. Then click Edit or the pencil icon. 


If you see that everything is set accordingly, I recommend contacting our payroll support. This way, they can investigate what's the cause of this concern, and they'll be able to explain why this is happening. 


Here's how: 


  1. In your QBO account, select Help (?)
  2. Choose the Search tab.
  3. At the bottom of your screen, click Contact Us.  
  4. Type your concern. Then click Continue
  5. You may choose CallbackAppointment, or Chat as your way to connect with us. 
  6. Kindly fill out the provided field such as your First nameLast nameEmail address, and Phone number. 
  7. Depending on what you choose as your way to connect with us, click CallbackSchedule an appointment, or Chat. 


To know more about the available hours or our support, you can refer to this material: Contact Payroll Support


I'll leave this material for you to use in case you want to learn more about payroll tax filing: Set up or change your payroll tax filing or payment schedules


Let me know in the comment section if you have other QuickBooks-related concerns. We're always around to offer further assistance. 

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