If you run a payroll that’s only paying non-taxable money to an employee, such as an expense reimbursement, you should skip any pre-tax deductions for the employee. Pre-tax deductions should not come out of non-taxable pay. However, you can take pre-tax deductions when you pay an expense reimbursement on the same check with other taxable earnings.
For more information, see our help article Deduction Types.