How to Change Your Payroll Bank Account in QuickBooks Online

Where to find and change your payroll bank account

In QuickBooks Online, your payroll bank account lives in the payroll settings, not in your general chart of accounts. To change it, go to the Payroll Settings menu (found under the gear icon in the top right), then select Payroll Settings again from the dropdown. From there, click the Payroll Account tab on the left side. You will see the bank account currently linked to payroll — this is the account QuickBooks pulls money from when you run payroll.

Click Edit next to the account name. A dropdown menu will appear showing all the bank accounts you have already set up in QuickBooks. Select the new account you want to use for payroll, then click Save. The change takes effect when ready, but only for payroll runs you process after you make the change.

If the bank account you want to use does not appear in the dropdown, you will need to add it to QuickBooks first. Go to Chart of Accounts (under the Accounting menu), click New, select Bank as the account type, enter your bank details, and save. Then return to Payroll Settings and select it from the dropdown.

Key Takeaways

Your payroll bank account is separate from your general business accounts and lives in Payroll Settings, not in your chart of accounts.
Changing the account takes two steps: go to Payroll Settings, find the Payroll Account tab, and select a new account from the dropdown.
The new account must already exist in your QuickBooks chart of accounts before you can link it to payroll.
Changes take effect when ready for future payroll runs, but do not affect payroll you have already processed.

Why you might need to change your payroll account

The most common reason to change your payroll bank account is that you have opened a new business bank account and want payroll to draw from that instead. This often happens when you separate payroll funds from operating funds, or when you switch banks entirely and need to point QuickBooks to your new account number.

Another reason is correcting a mistake — if you initially linked the wrong account to payroll, changing it prevents future payroll runs from pulling from the wrong place. A third reason is consolidation: if you have been running payroll from multiple accounts and want to centralize everything into one account, you would change the payroll setting to point to that single account.

Changing the account does not move money that has already been paid out. It only affects which account QuickBooks will debit when you process payroll going forward.

What happens to past payroll when you change the account

Past payroll runs remain tied to the account they were originally processed from. QuickBooks keeps a record of which account was used for each payroll run, and that record does not change when you update your payroll settings. This means your payroll history and bank reconciliation will still show the old account for those transactions.

If you need to move money between accounts to match what QuickBooks shows, you will do that through your bank, not through QuickBooks. For example, if you processed payroll from Account A but now want all payroll to come from Account B, you would manually transfer funds from A to B at your bank to keep your accounts balanced.

Adding a new bank account if it does not exist yet

If you have a new bank account that is not yet in QuickBooks, you cannot select it in the payroll dropdown until you add it. Go to Accounting in the left menu, then click Chart of Accounts. Click the New button in the top left corner.

Select Bank as the account type. Enter the account name (for example, "Payroll Operating Account"), your bank name, and your account number. You can leave the opening balance at zero if the account is brand new, or enter the current balance if it already has money in it. Click Save and Close.

Once the account is saved, return to Payroll Settings and follow the steps in the first section. The new account will now appear in the dropdown menu.

Timing: when the change takes effect

The change to your payroll bank account is when ready in QuickBooks, but the timing of when it actually affects your bank depends on when you next run payroll. If you change your payroll account on a Tuesday and do not run payroll until Friday, the Friday payroll will pull from the new account. Any payroll you have already processed will have already pulled from the old account.

If you are in the middle of a payroll period and have already processed some paychecks from the old account, those paychecks will not be reversed or re-run. Only new payroll runs will use the new account. This is why it is important to make the change before you process payroll for the next period, not after.

Checking which account is currently linked

To verify which account is currently set up for payroll, go back to Payroll Settings and click the Payroll Account tab. The account name will be displayed at the top. If you are not sure whether a change has taken effect, this is where to check.

You can also see which account was used for a specific payroll run by opening that payroll record. Click Payroll in the left menu, then Payroll History. Find the payroll run you want to check, click on it, and scroll down to see the account that was debited.

Troubleshooting: account does not appear in the dropdown

If the bank account you want to use does not show up in the payroll dropdown, it is because it has not been added to your chart of accounts yet. Follow the steps in the "Adding a new bank account" section above to create it first.

Another reason an account might not appear is if it is marked as inactive in your chart of accounts. Go to Chart of Accounts, find the account, click the three dots next to it, and select Make Active. Then return to Payroll Settings and try again.

Frequently Asked Questions

Can I use a different bank account for each employee?

No. QuickBooks Online payroll pulls all employee paychecks from a single account that you set in Payroll Settings. If you need to split payroll across multiple accounts, you would need to process separate payroll runs for different groups of employees, changing the payroll account between each run. Most businesses do not do this — it is simpler to pull all payroll from one account and then transfer funds between accounts at the bank level if needed.

What if I change the payroll account but forget to update it before processing payroll?

QuickBooks will process payroll using whichever account is currently set in Payroll Settings at the time you run payroll. If you realize the mistake after payroll has been processed, you cannot undo it through QuickBooks. You would need to contact your payroll processor or bank to reverse the transaction, then reprocess payroll from the correct account.

Does changing the payroll account affect tax payments?

No. Tax payments are separate from payroll and have their own settings. Changing your payroll bank account only affects where employee paychecks are drawn from, not where tax deposits are sent. You would change tax payment accounts in a different section of Payroll Settings if needed.

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

Yes, you can change it at any time. The change takes effect the next time you process payroll. If you have already processed some paychecks in the current period from the old account, those will not be affected. Only future payroll runs will use the new account.

This guide is for general information only and is not medical, financial, legal, or other professional advice. For decisions specific to your situation, consult a qualified professional. See our Editorial Policy.