What is the best way to pay an employee the money that is being withheld from their direct deposit for a pretax HSA account? I am using QB Online.

Hi, @cca8. It's great having you here in the QuickBooks Community. 

If you're refunding your employee with withheld direct deposit for a pretax HSA account, our Payroll Support team can assist you best. I'm here to add further details about this and on how you can reach out to them.

Refunding your employee for a withheld pretax HSA account through direct deposit will need assistance from our Support Team since this also involves correcting previous paychecks. They can also guide on the next steps to take. Here' show you can reach out to them:

1. Sign in to your QBO account.
2. Go to Help (?).
3. Select Contact Us.
4. Enter your concern, then select Let's talk.
5. Choose a way to connect with us:
   • Start a chat with a support expert.
   • Get a callback from the next available expert.

After correcting your previous paychecks, create an unscheduled payroll to refund your employee of the withheld pretax HSA account.

1. Go to Payroll. Then, select Employees.
2. Select the dropdown, and select one of the following options: Bonus only, Commission only or Fringe benefits only.
3. Supply the necessary info about taxes or paycheck calculations based on your selection. Once complete, select Continue. 
4. Select or review the pay period and pay date. Then, select the employee you'd like to pay.
5. Click on the three dotted vertical icon. Then, select Edit paycheck to enter your pay details. You can enter other paycheck info as necessary.
6. Select Preview payroll.
7. Select or review the QuickBooks bank account to track your payroll.
8. Select Preview payroll details, Save for later or Submit payroll.
9. Select Close.

To ensure that the deduction items are correctly withheld from your employee's paycheck, you can run the Payroll Details report after your next payroll. Let me add this article as a guide: Run payroll reports.

We'll be here in the Community if you need further assistance setting up HSA contribution in QBO. We're committed to offering ongoing support.