Change your bank account in QuickBooks Desktop by updating the account link in your payroll settings

QuickBooks Desktop stores your payroll bank account information in two places: in your payroll settings and in the actual bank account record itself. To change which account your payroll deposits come from, you need to update both. The process takes about five minutes and does not affect your employees' paychecks — it only changes where the money comes from on your end.

Before you start, have your new bank account number and routing number ready. You will also need to know whether you are switching to a completely different bank or just a different account at the same bank, because the steps differ slightly.

Key Takeaways

  • Update your payroll bank account in QuickBooks Desktop through Employees > Payroll Settings > Bank Accounts, not through your regular chart of accounts.
  • You must change the account in two places: the payroll settings and the bank account record itself, or your paychecks will pull from the wrong account.
  • If you are switching banks entirely, you may need to set up a new bank account record in QuickBooks before you can link it to payroll.
  • Your employees see no change — the account switch only affects which of your accounts the payroll deduction pulls from.
  • Test the change with a small manual paycheck before running your next full payroll to make sure the account link is correct.

Update the payroll bank account in your payroll settings

Open QuickBooks Desktop and go to the Employees menu at the top. Click Payroll Settings, then click Bank Accounts on the left side of the window that opens.

You will see a list of any bank accounts you have already linked to payroll. Find the account you are currently using and click the pencil icon (Edit) next to it. A small window will open showing the account details.

If you are switching to a different account at the same bank, click the dropdown menu next to "Account" and select the new account from the list. If the new account does not appear in the dropdown, you will need to set it up in QuickBooks first — see the section below on adding a new bank account.

Click OK to save the change. This updates your payroll settings, but you still need to change the account record itself.

Change the account record in your chart of accounts

Go to Lists at the top menu and click Chart of Accounts. Find the bank account you just changed in the payroll settings. Right-click on it and select Edit Account.

In the Account window, look for a field labeled "Account Number" or similar. Make sure this matches the account number of the bank account you want to use for payroll. If you are switching to a new account, update this field with the correct account number.

Click OK to save. Now your payroll settings and your account record are pointing to the same account.

Set up a new bank account if you are switching banks

If the account you want to use does not exist in QuickBooks yet, you need to create it before you can link it to payroll. Go to Lists > Chart of Accounts and click the Account button at the bottom left. Select New.

Choose Bank Account as the account type. Give the account a name that matches your bank statement — for example, "Checking - First National" — so you can recognize it later. Enter your new account number in the Account Number field.

Leave the "Bank Account Number" field blank unless your bank has given you a specific code for QuickBooks. Click OK to create the account. Now you can go back to your payroll settings and select this new account from the dropdown.

Test the change before running payroll

Before you run your next full payroll cycle, create a single test paycheck to make sure the account link is working. Go to Employees > Pay Employees and create a paycheck for one employee with a small amount.

When you click Create, QuickBooks will show you which account the payroll deduction will pull from. Verify that it is the correct account. If it is wrong, go back to your payroll settings and check the account link again.

You can delete the test paycheck afterward — just go to Employees > Pay Employees, find the test check, and delete it before you submit payroll. This step prevents mistakes that could overdraft the wrong account or delay paychecks.

What happens if you change the account mid-payroll cycle

If you change your payroll bank account after you have already created paychecks for the current cycle, those paychecks will still pull from the old account. Only paychecks created after you make the change will use the new account.

If you need to move paychecks that were already created, you will have to delete them and recreate them after you update the account. This is why it is best to change your payroll account at the start of a payroll cycle, before you create any paychecks.

Frequently Asked Questions

Do my employees need to do anything when I change the payroll bank account?

No. Your employees' direct deposit information stays the same — they receive their paychecks in their own accounts as usual. The change only affects which of your company accounts the payroll deduction comes from.

What if I accidentally set up the wrong account in payroll?

Go back to Employees > Payroll Settings > Bank Accounts, click Edit next to the wrong account, and select the correct one from the dropdown. Save the change and test with a small paycheck before running full payroll.

Can I use the same bank account for payroll and regular business expenses?

Yes, many small businesses do this. QuickBooks will track all transactions — payroll and non-payroll — in the same account. Just make sure you have enough balance to cover both.

What if my new bank account is not showing up in the dropdown?

The account must exist in your chart of accounts first. Go to Lists > Chart of Accounts, create a new bank account record with your new account number, and then go back to payroll settings. The new account should now appear in the dropdown.