Bonus payroll is only allowing paper cheques, not direct deposit, even though bi-weekly payroll is by direct deposit. Is there a way to change this?

Hi thannah.

Being able to pay your employee through direct deposit is a great way to get them paid fast with little effort on your end. I'd be happy to help you get the bonus cheques sent through direct deposit.

When you set up direct deposit for an employee it allows you to switch between paper cheque or direct deposit by selecting the payment method during creation. Here is an image of where to click.
 
If you don't see an option for direct deposit there I recommend making sure that the employee is set up for direct deposit by following these steps: Go to Payroll>Employees>Select the Employee>Click Edit Employee>Scroll to the bottom and make sure it says direct deposit. If it doesn't click the pencil under how do you want to pay and select direct deposit at the top drop down menu.

If they are set to be paid through direct deposit but you still cant select it for the bonus cheque I recommend reaching out to our support team using one of the following methods:

Schedule a Callback or start a Chat: click (?)Help in the upper right in QuickBooks Online > type and enter "Contact support" into the QB Assistant > click Contact Us > explain your situation > click Let's Talk > choose Get a callback or Start a Chat.
Social Media: Facebook, Twitter, and Instagram.
Support hours are from Monday to Friday between 9 a.m. and 8 p.m. ET.

Have a great day!