Payroll Account

Fix common payroll issues in QuickBooks Online

We know how important it is to keep your payroll running smoothly. Here are solutions to some common questions regarding payroll adjustments, account mapping, and system errors.

Correct over-withheld payroll taxes

If you need to refund an employee for over-withheld taxes, you must first record an adjustment in your payroll system. When you write the refund check to the employee, use the same offset account that you selected when you originally entered the adjustment. This ensures your books remain balanced.

Fix missing companies in your client list

If you are an accountant or payroll administrator and notice that a company is missing from your client selection list in Intuit Online Payroll, this may be a temporary system sync issue. If the problem persists, check for service alerts or contact our support team, as our engineers may need to investigate the connection between your account and the specific client file.

Resolve automatic salary account creation

If you see a new, unexpected numeric salary account appearing in your Chart of Accounts, it is likely due to the bank account mapping settings during the export from Intuit Online Payroll to QuickBooks Online. To fix this:

1. Log in to your Intuit Online Payroll account.
2. Go to the Setup tab.
3. Select Preferences under the Export section.
4. Verify that the correct bank account is selected for wages and taxes, and update it if necessary.

Separate combined payroll and operating accounts

If your payroll account and operating account are displaying on the same bank register despite being set up as two separate accounts, check your Chart of Accounts structure. This usually happens if the accounts were accidentally tied together under a common parent account or sub-account hierarchy. Ensure they are listed as distinct, top-level bank accounts to separate the registers.

Set up deductions for bonus checks

QuickBooks Online Payroll automatically calculates the appropriate tax deductions for bonus pay if you have set up the “Bonus” pay type correctly. To add or verify the Bonus pay type for an employee:

1. Go to the Workers or Employees menu.
2. Select the employee’s name.
3. Click the Edit (pencil icon) in the Pay section.
4. Click the edit icon next to the question “How much do you pay [employee name]?”
5. Select the Bonus item (check the box).
6. Click Done.

Track payroll by cost center

Yes, you can track payroll expenses by specific departments or cost centers, such as Marketing or Finance. While you cannot place the payroll bank account itself under a specific department, you can use Class Tracking to categorize payroll expenses.

1. Turn on Class Tracking in your Account and Settings.
2. Create classes for your departments (e.g., Marketing, Finance).
3. Assign the appropriate class to your payroll transactions to report on costs by department.

Troubleshoot Security Key errors

If you use the Security Key feature for extra protection, you may encounter an error (such as “ReferenceError: ‘auth’ is undefined” or a screen loop) when trying to edit sensitive direct deposit information. This is a known issue when the system attempts to verify your identity during specific changes.

If you experience this while trying to:

• Enter or change a bank account for an employee
• Add a new user to the payroll account
• Edit authorized user email addresses

We recommend temporarily disabling the Security Key feature to complete your update, or contacting support for assistance with the verification process.