Change your payroll bank account by going to Payroll Settings, selecting the account you want to replace, and linking a new one

QuickBooks Online stores the bank account where your payroll deposits go. If you switch banks, close an account, or want payroll to hit a different account, you change it in the Payroll Settings menu, not in your general chart of accounts. The process takes a few minutes and does not affect past payroll records.

The steps differ slightly depending on whether you use QuickBooks Payroll (the built-in service) or a third-party payroll processor linked through QuickBooks. Both routes are covered below, along with what to do if you have already run payroll on the old account.

Key Takeaways

  • Payroll bank accounts live in Payroll Settings, not in your chart of accounts, so changing them there does not affect your general accounting.
  • You can add a new bank account and mark the old one inactive without deleting it, which keeps your payroll history intact.
  • If you have already run payroll on the old account, you do not need to redo it — just change the account for future pay runs.
  • Third-party payroll processors (like Gusto or ADP) linked to QuickBooks may require you to change the account in their own dashboard first, then sync it back to QuickBooks.
  • Your bank may take one to three business days to recognize the new account for direct deposit, so plan the change before your next payroll date.

Steps to change the account in QuickBooks Payroll

Open QuickBooks Online and go to the Payroll menu on the left sidebar. Click Settings (the gear icon), then select Payroll Settings. You will see a list of accounts currently linked to payroll.

Find the account you want to replace and click the Edit button next to it. A window will open showing the account details. Click Unlink Account or Remove, depending on your version. QuickBooks will ask you to confirm — this does not delete the account from your chart of accounts, only from payroll.

Once removed, click Add Account or Link Account in the same Payroll Settings screen. QuickBooks will prompt you to choose an existing bank account from your chart of accounts or to add a new one. If you have already set up the new bank account in your chart of accounts, select it from the dropdown. If not, you can create it here by entering the bank name, account type, and account number.

After you link the new account, QuickBooks will ask you to verify it. Some banks require you to confirm two small deposits (usually under $1 each) that QuickBooks sends to the account. Check your bank statement in one to two business days and enter those amounts back into QuickBooks to complete verification. Until verification is done, payroll will not process to that account.

Changing the account if you use a third-party payroll processor

If you use Gusto, ADP, Paychex, or another payroll service that connects to QuickBooks, the bank account is usually managed in that processor's dashboard, not in QuickBooks itself. QuickBooks pulls the information from the third-party service, so changing it in QuickBooks alone will not work.

Log into your payroll processor's account and find the payroll bank account settings (often under Company Settings, Payroll Settings, or Banking). Remove the old account and add the new one there. Most processors will ask you to verify the new account the same way QuickBooks does — by confirming small test deposits.

Once the account is verified in your payroll processor, return to QuickBooks Online and go to Payroll Settings. The new account should sync automatically within a few hours. If it does not appear, click Sync or Refresh (the exact button name varies by processor). If it still does not show, contact your payroll processor's support team — they may need to push the change from their end.

What happens to payroll you have already run

Changing your payroll bank account does not affect pay runs you have already completed. If you ran payroll last week on the old account, those deposits already went out and will not be reversed or rerouted. The change only applies to future pay runs.

If you realize you need to change the account before you have submitted payroll to your bank, you can edit the pay run. Go to Payroll, click Pay Employees, find the pay run that has not yet been submitted, and click Edit. You can change the account there before you send it to the bank.

Timing: when to change the account before payroll

Banks typically take one to three business days to recognize a new account for direct deposit after you link it in QuickBooks. If your payroll is due on Friday, change the account by Wednesday at the latest to give the bank time to process it.

If you are cutting it close, contact your bank's payroll or ACH department directly and ask them to confirm the account is active for incoming transfers. Some banks flag new accounts as inactive until they receive their first deposit, which can cause payroll to bounce.

If payroll does bounce because the account was not ready, your payroll processor will usually hold the funds and ask you to confirm a working account. You will not lose the money, but your employees' deposits will be delayed. This is another reason to make the change at least a few days before payroll is due.

Keeping the old account in your records

You do not have to delete the old bank account from your chart of accounts. Instead, you can mark it as inactive, which keeps all the payroll history tied to it but removes it from dropdown menus and reports.

To mark an account inactive, go to your Chart of Accounts (not Payroll Settings), find the old bank account, click the three-dot menu next to it, and select Make Inactive. The account will stay in QuickBooks and all past transactions will remain, but it will not appear in active account lists. This is useful for auditing and for keeping a complete record of where payroll went in previous years.

Troubleshooting: account will not link or verify

If QuickBooks will not let you link the new account, check that the account exists in your chart of accounts first. If it does not, create it: go to Chart of Accounts, click New, select Bank as the account type, enter the account details, and save it. Then return to Payroll Settings and try linking it again.

If the account is in your chart of accounts but still will not link, the account number or routing number may be incorrect. Double-check both against your bank statement or your bank's website. If they are correct and it still will not link, log out of QuickBooks, clear your browser cache, and log back in. If the problem persists, contact QuickBooks support — there may be a temporary issue with the bank's connection.

If verification is stuck (QuickBooks is waiting for you to confirm the test deposits), make sure you are checking the correct bank account. The test deposits go to the account you linked, not to your main operating account. Log into the bank account itself and look for two small deposits from Intuit or QuickBooks. If you do not see them after three business days, contact your bank to ask if they are holding them, then contact QuickBooks support.

Frequently Asked Questions

Can I have payroll go to two different bank accounts?

QuickBooks Online allows only one payroll bank account at a time. If you need to split payroll between two accounts (for example, one for salary and one for contractors), you will need to run separate pay runs for each group and manually change the account between them, or use a third-party payroll processor that supports split deposits.

What if I change the account but forget to verify it before payroll is due?

Payroll will not process until the account is verified. If you are close to your payroll date, contact QuickBooks support and ask if they can expedite verification, or temporarily link your old account back, run payroll, and then switch to the new account for the next cycle.

Do I need to tell my employees about the bank account change?

No. Employees receive direct deposits to the account you set up in QuickBooks — they do not need to do anything on their end. The change is invisible to them as long as payroll deposits on time. If there is a delay because the account was not verified, you may want to notify them.

Can I change the payroll account in the middle of a pay period?

Yes, but only if you have not yet submitted the pay run to your bank. If you have already submitted it, the deposits will go to the old account and you cannot redirect them. For future pay runs, the new account will be used automatically.

What if my new bank account is at a different bank entirely?

The process is the same. Create the new bank account in your chart of accounts with the correct routing number and account number, then link it in Payroll Settings. QuickBooks will send test deposits to verify it, just as it does for accounts at the same bank. Make sure your new bank is set up to receive ACH transfers before you link it.