To record QSEHRA or ICHRA reimbursements in Paychex, add the approved reimbursement amount from your Take Command Reimbursement Statement as a non-taxable employer reimbursement in your payroll system and include it in the employee's payroll run.
Before you process reimbursements
Before entering reimbursements into Paychex:
Log in to your Take Command Admin Portal.
Download your latest Reimbursement Statement.
Review the approved reimbursement amount for each employee.
Verify that all reimbursement amounts match the approved statement.
Only reimburse amounts that appear on the Take Command Reimbursement Statement.
How to record reimbursements in Paychex
Option 1: Create a recurring non-taxable reimbursement
For employees receiving the same reimbursement amount each pay period:
Open the employee's payroll profile in Paychex.
Add a reimbursement or earnings code designated for non-taxable employer reimbursements.
Enter the approved reimbursement amount from the Take Command statement.
Save the recurring payroll item.
Verify the reimbursement appears correctly on the next payroll run.
This approach works well for employees receiving recurring premium reimbursements.
Option 2: Enter a one-time reimbursement
For reimbursement amounts that change from month to month:
Start your payroll run.
Open the employee's payroll record.
Add the reimbursement amount for that payroll period.
Confirm the reimbursement is classified as non-taxable.
Complete payroll processing.
This option is commonly used when employees submit varying medical expenses each month.
How should QSEHRA and ICHRA reimbursements be taxed?
Most QSEHRA and ICHRA reimbursements are non-taxable when:
The HRA is compliant
The employee has qualifying coverage
The reimbursement is for an eligible expense
Non-taxable reimbursements generally:
Are excluded from employee taxable wages
Are not subject to payroll taxes
Should not be treated as regular compensation in payroll processing
Are there any taxable reimbursements?
Yes, in limited situations.
For example, certain QSEHRA reimbursements involving premiums already paid pre-tax through a spouse's employer-sponsored plan may need to be treated as taxable income.
If you are unsure whether a reimbursement is taxable or non-taxable:
Review the reimbursement details in Take Command.
Consult your payroll provider or tax advisor.
Verify the reimbursement classification before processing payroll.
What if my reimbursement amounts change each month?
Reimbursement amounts can change because of:
Medical expense claims
Allowance adjustments
Carryover balances
New employee enrollments or terminations
You should review the latest Take Command Reimbursement Statement before every payroll run rather than relying on prior payroll amounts.
What information does Take Command provide?
Take Command provides:
Approved reimbursement amounts
Employee reimbursement reports
Allowance and carryover information
Downloadable reimbursement statements
Take Command does not transmit reimbursement payments to employees. Employers remain responsible for issuing reimbursements through payroll or another payment method.
What if I need help with Paychex setup?
Paychex controls its payroll configuration and reimbursement codes.
If you need help:
Log in to your Paychex administrator account.
Contact your Paychex payroll representative.
Ask how to configure a non-taxable employer reimbursement earning code for HRA reimbursements.
Paychex support can provide instructions specific to your payroll configuration.