
Processing a Special Pay Run as Paper Checks (4-Step Run)

Sometimes you may need to pay employees with a paper check instead of using direct deposit through Beyond.
This could happen if:
- An employee hasn’t enrolled in direct deposit.
- You paid a contractor on the spot by check.
- You issued paper checks because payroll wasn’t processed on time.
To make this easier, you can even print checks using check stock.
(Note: You must be approved to issue paychecks by direct deposit. Beyond does not print paper checks on your behalf.)
Since unexpected situations come up — and because there’s no extra cost to running additional payrolls — it’s helpful to know how to process a one-off special pay run.
Want to learn more about special pay runs?
Just looking to issue a bonus (like a year-end bonus)?
If you signed up with Beyond after December 6, your account is already configured with the new 3-step pay run.
Step 1: Adjust Pay Run Settings
At the top of the payroll page, you’ll see your current settings. Click any item to make changes.
- Update the pay period and check date as needed.
- If you’ve already handed out paper checks, select “Hold all direct deposits and process as paper checks?”
Be sure not to hold employee deductions.
Step 2: Select Employees Paid by Paper Check
Choose the employees who received (or will receive) paper checks.
- Use Uncheck All if you only need to pick a few employees.
Step 3: Review Payroll
Once your selections and settings are ready, review payroll as usual:
- Verify wages, deductions, and withholdings.
- Confirm accuracy before approving.
Step 4: Approve Payroll
Approve the payroll just like a normal run. Employees marked as “Paper check” will be excluded from direct deposit.
Our Tax Accuracy Guarantee
At Beyond, we take payroll tax accuracy very seriously. Our Tax Accuracy Guarantee ensures that we’ll always back our calculations, filings, and payments.
Here’s what you need to know:
- You are responsible for providing accurate company and employee information, including IDs, work locations, and tax rates.
- Beyond guarantees the accuracy of our calculations and the filings/payments we make based on the information you provide.
- In rare cases, we may need additional details or request action from you. If this information isn’t provided, affected filings and payments will not be covered by the guarantee.
Need Help?
If you still have any questions, please don’t hesitate to reach out. Our team will be happy to provide answers and assist you in any way we can.