Hi, TPF4. Yes, you can mark the check as Void to ensure that the transaction remains in your records with a value of $0 for accurate payroll documentation and tax calculations.
Here's how:
- Open your QuickBooks.
- Go to Payroll and select Employees.
- Under Run payroll, select the Paycheck list in the upper right corner of your screen.

- Pick the affected paychecks.
- In the Actions column, click the Dropdown and choose Void.

- Confirm your selected action and select Save.
Also, ensure that the employee's payment method is Direct Deposit. The reason it creates a check instead is that the setup is not a Direct Deposit. To change the employee's payment method to direct deposit, here's how:
- Go to Employees and select the affected Employee.
- In the Payment Method section, click Edit.

- In the Payment Method dropdown, choose Direct Deposit.

To answer your second question, yes you can re-run a Direct Deposit payroll again after you perform the steps I provided. When re-running the Direct Deposit payroll, you must submit it before the cutoff time to ensure the funds are processed on time.
You can check this article to determine what your direct deposit lead time is and when to submit or approve payroll when you already know what your payroll lead time is: When to send your direct deposit payroll.
Let us know if you need anything else. Have a good one.