Update your bank account details in QuickBooks Online payroll settings

To change the bank account QuickBooks Online uses to pay your employees, go to Payroll Settings in the left menu, then select Payroll Account. You'll see the bank account currently linked to payroll. Click Edit next to that account, then choose a different bank account from your list of connected accounts, or add a new one. Save your changes. The new account takes effect on your next payroll run.

If you don't see the account you want to use, you may need to connect it to QuickBooks first. Go to Banking in the left menu, select Connected Accounts, and add your bank using your online banking login. Once the account appears in your QuickBooks account list and has been verified by your bank (usually one to two business days), it will show up as an option in Payroll Settings.

Changing the payroll account does not affect past payroll records or tax filings. QuickBooks keeps a history of which account was used for each payroll run. Your employees' direct deposit information stays the same—only the source account changes.

Key Takeaways

  • Access payroll bank account settings through Payroll Settings > Payroll Account, then click Edit to select a different connected account.
  • New bank accounts must be connected to QuickBooks through the Banking section and verified by your bank before they appear as payroll options.
  • The change takes effect on your next payroll run and does not alter employee direct deposit setup or past payroll history.
  • If you're switching accounts because of a banking change, update your payroll account before you run payroll to avoid payment delays.

When you need to add a new bank account first

If the bank account you want to use is not yet connected to QuickBooks, you cannot select it in Payroll Settings until you add it. Go to Banking in the left menu and click Connected Accounts. Select your bank from the list, or search by name. You'll be asked to log in with your online banking credentials. QuickBooks will verify the connection with your bank, which usually takes one to two business days.

During verification, your bank may send a small test deposit to the account you're connecting. Check your bank statement and enter the deposit amount in QuickBooks to confirm ownership. Once verified, the account is ready to use for payroll. If verification takes longer than expected, contact your bank's customer service—some banks require you to enable third-party connections in your security settings first.

Timing: when the change takes effect

The new bank account becomes your payroll account immediately after you save the change in Payroll Settings. However, it only affects payroll runs you create after the change. If you've already created a payroll run for the current pay period, it will still draw from the old account. To use the new account for the current pay period, you must delete the payroll run, update the account, and create a new one.

If you're close to your payroll deadline, make the change as soon as possible. Payroll processing and bank transfers take time—ACH transfers typically clear within one to two business days. If you change accounts the day before payday, there's a risk the transfer won't reach your employees on time. Plan the change for early in your pay period when possible.

What happens to employee direct deposit information

Changing your payroll bank account does not change where your employees' paychecks go. Their direct deposit routing and account numbers remain exactly the same. The change only affects which of your company's accounts the money comes from. Employees will not see any difference in their paychecks or deposit timing.

If an employee's direct deposit information needs to change—because they switched personal banks, for example—that's a separate update. Go to the employee's record, click Employment, then Direct Deposit, and update their banking details there. This change is independent of your company's payroll account.

Fixing a failed payroll transfer

If a payroll run fails because the bank account has insufficient funds or was closed, QuickBooks will show an error message in the payroll summary. The most common fix is to change the payroll account to one with available funds, then retry the transfer. Go to Payroll Settings, update the account, and return to the failed payroll run. Click Retry to attempt the transfer again from the new account.

If the account was closed or compromised, update it immediately and retry before your payroll deadline passes. If the retry still fails, contact your bank to confirm the account is active and has no blocks on ACH transfers. Some banks require you to call and authorize payroll transfers manually, especially if the account is new or has had no recent activity.

Keeping payroll records accurate after a change

QuickBooks maintains a complete record of which account was used for each payroll run, so your tax filings and audit trail remain accurate even after you change accounts. The IRS and state tax agencies see the total payroll amounts, not the source account. Your accountant or bookkeeper can pull a payroll history report that shows all transfers by date and account if needed.

If you're changing accounts because of a merger, acquisition, or business restructuring, document the change date in your records. This helps if you're ever audited and need to explain why payroll came from different accounts in different periods. QuickBooks' payroll reports include the account used, so the documentation is built in.

Frequently Asked Questions

Can I use a business savings account for payroll instead of checking?

Yes, as long as the account is connected to QuickBooks and your bank allows ACH transfers from it. Most business savings accounts support payroll transfers, but some banks restrict ACH activity on savings accounts. Check with your bank before you connect the account. If transfers are blocked, you may need to move money to a checking account first or request that your bank enable ACH on the savings account.

What if I accidentally ran payroll from the wrong account?

If payroll was processed but not yet transferred to your bank, you can delete the payroll run, update the account, and create a new one. If the transfer already cleared, contact your bank to reverse it, then run payroll again from the correct account. This usually takes three to five business days. Notify your employees if there's any delay in their deposits.

Do I need to tell my employees when I change the payroll account?

No. The change is internal to your company and does not affect where their paychecks are deposited. Their direct deposit information stays the same. You only need to notify them if there's a delay in payroll processing or if their deposit timing changes for any reason.

Can I split payroll between two bank accounts?

QuickBooks Online payroll draws from a single account per payroll run. You cannot split one payroll across two accounts. If you need to fund payroll from multiple sources, transfer money to your primary payroll account first, then run payroll from that account.