QuickBooks relies on the information you've set up, Peter. Let’s double-check your employees' payment methods to ensure they'll be paid correctly.
Once you've set up an employee for direct deposit, running payroll will automatically use that method. However, it’s important to verify that the payment method is not mistakenly set to paper check, as this would prompt QuickBooks to issue a check instead. To check the payment method, follow these steps:
- Navigate to the Employees from the Payroll section.
- Review the payment methods in the Pay Method column.

If verified that an employee is set to receive a paper check, you can change their payment method to direct deposit.
If the issue persists, please reach out to our Live Support Team. They have the necessary tools to check for any possible bank holds that can cause QuickBooks to issue a paper check instead.
Additionally, if you need to change your existing payroll bank account, please refer to this article: Change your payroll bank account.
If you're interested in streamlining your payroll process to have a multi-state filing and to have an expert setup review, you can Explore QuickBooks Payroll.
We're here to help if you need further assistance managing your employee information or have other QuickBooks-related concerns. Have a great day.