Where to find and change your payroll bank account

In QuickBooks Desktop, your payroll bank account lives in the Payroll Setup wizard or in your Chart of Accounts. To change it, you open QuickBooks, go to the Employees menu, select Payroll Setup, and work through to the Bank Account section. If you have already set up payroll, you can also change it directly by editing your Chart of Accounts — find the bank account you currently use for payroll, and swap it for the new one.

The reason you need to do this is straightforward: QuickBooks tracks which bank account your payroll checks and direct deposits come from. If you switch banks or open a new account for payroll, QuickBooks still points to the old one unless you tell it otherwise. This matters because your payroll register will show deposits going to the wrong place, and your bank reconciliation will not match.

The process takes about five minutes if you know where to look, and you do not need to redo your entire payroll history — just update the account going forward.

Key Takeaways

  • Your payroll bank account is set in the Payroll Setup wizard under the Employees menu, or directly in your Chart of Accounts.
  • Changing it does not erase past payroll records; it only affects which account future paychecks are drawn from.
  • You will need the routing number and account number of your new bank account before you start.
  • After you change the account, run a test payroll or direct deposit to confirm QuickBooks is pulling from the correct bank.

Using the Payroll Setup wizard to change your bank account

If you are still in the initial payroll setup phase, the Payroll Setup wizard walks you through step by step. Click Employees at the top menu, then Payroll Setup. The wizard opens with tabs across the top: Company, Employees, Taxes, and Bank Account. Click the Bank Account tab.

From there, QuickBooks shows you the account it currently has on file. You can edit it right there — change the account number, routing number, or select a completely different bank account from your Chart of Accounts. If your new account is not yet in QuickBooks, you will need to add it to your Chart of Accounts first (go to Lists, Chart of Accounts, and create a new bank account), then come back to Payroll Setup and select it.

Once you have entered the new account details, click Next and finish the wizard. QuickBooks saves the change when ready.

Changing the account if payroll is already running

If you have been running payroll for a while and need to switch accounts mid-year, the process is slightly different. Go to Lists at the top menu, then Chart of Accounts. Find the bank account you currently use for payroll — it will usually be named something like "Payroll Bank Account" or "Checking Account."

Right-click on that account and select Edit Account. You can change the account number and routing number here, or you can select a different account entirely from the dropdown. If you want to move payroll to a bank account that already exists in your Chart of Accounts, you can do that too — just make sure the old account is no longer marked as your payroll account before you switch.

After you save the change, the next payroll run will pull from the new account. Your past payroll records stay where they are — they do not move or disappear.

What information you need before you start

Have your new bank account details in front of you. You will need the routing number (a nine-digit code that identifies your bank) and your account number (the number of the specific account at that bank). Both are printed on the bottom left of your checks, or you can call your bank and ask.

If you are setting up direct deposit for employees, you will also need to know whether your new bank supports ACH transfers — most do, but some smaller banks or credit unions have limits. Call your bank and ask if they can handle payroll direct deposits. They will tell you if there are any setup fees or if you need to sign anything.

You do not need to notify QuickBooks or your payroll processor separately — changing it in QuickBooks is the only step you need to take on the software side.

Testing your change before you run payroll

After you change the account, do not run your next payroll when ready. Instead, create a test payroll for one employee with a small amount — say, one dollar. Run it and check that QuickBooks shows the payment coming from your new bank account, not the old one. Look at the payroll register (Employees menu, Payroll Center, then Payroll History) and confirm the account name is correct.

If you are using direct deposit, run the test and watch for the ACH file to be created. If you are printing checks, print one test check and make sure it is drawn on the new account number. Once you confirm everything is correct, you can run your regular payroll.

This step takes ten minutes and saves you from discovering a mistake after you have already paid your whole team from the wrong account.

What happens to old payroll records when you switch

Your past payroll records do not change. If you ran payroll from Account A for six months and then switch to Account B, QuickBooks keeps all those old payments tied to Account A. Your payroll register, your tax reports, and your year-to-date totals all stay the same. Only new paychecks go to Account B.

This is actually helpful for your year-end accounting and tax filing, because everything stays in its original place. Your accountant or bookkeeper will see a clear record of which account was used when, which makes reconciliation easier.

Troubleshooting if the change does not stick

If you change the account but QuickBooks keeps pulling from the old one, the most common reason is that you changed the account details but did not save the change. Go back to Payroll Setup or Chart of Accounts, make the change again, and click Save or Next — do not just close the window.

The second most common issue is that you have multiple bank accounts in your Chart of Accounts and QuickBooks is confused about which one is the payroll account. Go to Lists, Chart of Accounts, and look at each bank account. Find the one marked as your payroll account (it will have a note or flag), and make sure it is the one you want. If not, edit it and change which account is designated for payroll.

If you are still stuck, restart QuickBooks completely. Close the program, wait ten seconds, and open it again. Sometimes the software needs a fresh start to recognize account changes.

Frequently Asked Questions

Do I have to change my payroll account if I switch banks?

Not when ready, but you should. If you do not update QuickBooks, your payroll register will show payments going to your old account, which will confuse your bookkeeping and make bank reconciliation impossible. Change it as soon as your new account is open and ready to receive deposits.

Will changing the account affect my tax filings or year-to-date totals?

No. Your payroll tax records and year-to-date earnings are tied to your employees and the payroll runs themselves, not to the bank account. Changing the account only changes where the money comes from — it does not touch your tax history or employee records.

What if I want to use different bank accounts for different employees?

QuickBooks Desktop does not support splitting payroll across multiple accounts in the standard setup. All employees' paychecks come from the same account. If you need to use different accounts for different purposes, you would need to run separate payroll batches or use a workaround with your accountant.

Can I change the account while a payroll is in progress?

You can, but do not. Finish the payroll you are currently running, confirm it has been processed and deposited, and then change the account. Changing it mid-payroll can cause the system to pull from the wrong account or create duplicate records.