Update Your Bank Account in QuickBooks Desktop Payroll
To change the bank account that QuickBooks Desktop uses to pay employees, open your company file and go to Employees menu, then select Payroll Settings. Click the Company tab, then Payroll, and you will see a section for Payroll Account. Select the new bank account from the dropdown list. QuickBooks will use this account for all future payroll runs unless you change it again.
The account you choose must already exist in your chart of accounts as a bank account type. If you have not yet added the new bank account to QuickBooks, you will need to create it first through Lists > Chart of Accounts before you can select it in payroll settings.
This change takes effect immediately for payroll checks you have not yet written. If you have already created paychecks in the current payroll cycle using the old account, those checks will still draw from the original account. You do not need to void and recreate them unless you want to.
Key Takeaways
- The payroll account setting is found in Employees > Payroll Settings > Company tab > Payroll section.
- Your new bank account must exist in your chart of accounts before you can select it as the payroll account.
- Changing the payroll account affects only paychecks you create after the change; existing paychecks remain tied to the old account.
- If you use online payroll services through QuickBooks, you may need to update your banking information separately with that service.
- Always verify the new account number and routing number are correct before running payroll to avoid payment delays.
Creating a New Bank Account in QuickBooks First
If the bank account you want to use does not yet appear in QuickBooks, you must add it to your chart of accounts before you can assign it to payroll. Go to Lists > Chart of Accounts, then click Account at the bottom left and select New.
Choose Bank as the account type. Enter the account name (for example, "Payroll Checking Account"), the account number, and the bank name. You can also enter the routing number and other details if you want QuickBooks to match transactions later. Click Save & Close.
Once the account is saved, it will appear in the dropdown when you return to Payroll Settings. You do not need to transfer money between accounts in QuickBooks itself — you only need the account to exist so QuickBooks knows where to record the payroll expense.
Updating Bank Details if You Use QuickBooks Payroll Services
If you use QuickBooks Payroll (the online service that processes and deposits paychecks automatically), changing the account in Desktop is only half the step. You must also update your banking information in the QuickBooks Payroll portal itself, or the service will continue trying to withdraw funds from your old account.
Log into your QuickBooks Payroll account online. Go to Settings or Company Settings, find the section for Bank Account or Funding Account, and update it there. You will usually need to provide the new account number and routing number, and QuickBooks may verify the account by depositing two small test amounts that you will need to confirm.
Do this update at least three to five business days before your next payroll run. If you change the account too close to payday, the payroll service may not have time to verify the new account and your payroll could be delayed.
What Happens to Paychecks Already Created
Paychecks you have already written in the current payroll cycle will continue to draw from the original bank account, even after you change the payroll account setting. QuickBooks does not retroactively reassign paychecks to a new account.
If you have written paychecks using the old account and you want them to come from the new account instead, you will need to void those paychecks and create new ones. To void a paycheck, open it, click Edit, then Void. This removes the transaction from your records. Then create new paychecks with the updated payroll account setting.
Voiding and recreating paychecks is usually only necessary if you have not yet printed or distributed them. If employees have already received paychecks, voiding them can create confusion and extra work for payroll reconciliation.
Verifying the Change Before Payroll Runs
After you change the payroll account, create a test paycheck to confirm QuickBooks is using the correct account. Go to Employees > Pay Employees, select one employee, and create a paycheck for a small amount or zero dollars. Do not print or process it yet.
Open the paycheck and look at the bottom of the form. You should see the new bank account name and number listed. If it still shows the old account, go back to Payroll Settings and confirm the change was saved. Sometimes QuickBooks requires you to close and reopen the company file for the change to take effect.
Once you confirm the correct account appears on the test paycheck, you can delete it (or void it if it was already saved) and proceed with your regular payroll run. This extra step takes two minutes and prevents the costly mistake of paying employees from the wrong account.
Troubleshooting: Account Does Not Appear in the Dropdown
If the new bank account you created does not show up in the Payroll Account dropdown, the most common reason is that QuickBooks does not recognize it as a bank account type. Go back to Lists > Chart of Accounts, find the account, and double-click it to open the details.
Check that the Account Type is set to Bank, not Checking, Savings, or another variation. Some versions of QuickBooks use different type names. If the type is wrong, change it to Bank, click Save & Close, and return to Payroll Settings. The account should now appear in the dropdown.
If the account still does not appear, close your company file completely and reopen it. QuickBooks sometimes needs to refresh its internal lists. After reopening, return to Payroll Settings and check the dropdown again.
Coordinating the Change with Your Bank
Changing the payroll account in QuickBooks does not automatically notify your bank. If you are switching to a new bank or a new account at the same bank, contact the bank directly to confirm they are ready to receive ACH transfers or check drafts from QuickBooks.
Provide your bank with the routing number and account number that QuickBooks will use. Ask the bank whether they require any setup, authorization forms, or advance notice before payroll can be processed. Some banks require you to pre-authorize ACH debits or to add QuickBooks as an authorized user.
If you are using QuickBooks Payroll (the online service), the service will contact your bank to verify the account during the setup process. You do not need to call the bank yourself in that case, but you should still confirm with your bank that they received and approved the verification requests.
Frequently Asked Questions
Do I need to update my payroll account if I only change banks but keep the same account number?
No, if your account number stays the same but the bank changes, you do not need to update QuickBooks. However, you should update the bank name in your chart of accounts for clarity. If the account number changes, you must create a new account in QuickBooks and update the payroll setting.
What if I accidentally run payroll from the wrong account?
Contact your bank immediately to stop the transaction if it has not yet cleared. If it has already cleared, you will need to transfer funds back to the correct account and reconcile your records. Going forward, use the test paycheck method described above to catch the error before it affects real paychecks.
Can I use different bank accounts for different employees?
No, QuickBooks Desktop payroll settings allow only one payroll account for the entire company. All employees are paid from the same account. If you need to pay different employees from different accounts, you will need to process those paychecks separately or use a different payroll system.
How long does it take for the new account to start working?
The change takes effect immediately in QuickBooks once you save it. However, if you use QuickBooks Payroll services, the online service may need three to five business days to verify the new bank account before it will process payroll from it. Check your Payroll settings online to see the verification status.
Do I need to update anything else when I change the payroll account?
If you use direct deposit, your employees' bank information does not change — they continue to receive deposits in their personal accounts. You only need to update the company's payroll account in QuickBooks and, if applicable, in your QuickBooks Payroll online settings.