Running a Special Payroll

Purpose

A special payroll is a pay run outside your regular payroll calendar (an "off-cycle" run). Use it to pay bonuses, severance, retroactive adjustments, or PTO payouts, or to pay employees for a pay period that was skipped because its regular payroll was not approved in time. This article also explains the Adjustment payroll, which starts from the same screen but moves no money.

Who can do this: Any user whose role includes the Payroll permission. This is usually the Employer Admin, but other admin roles can be granted the same access.

When to run a special payroll

• A regular pay period was skipped. Its pay date passed without approval.
• A missed punch or missed hours. An employee's hours (including PTO hours) did not make it into the regular run and it is already approved.
• Bonuses, discretionary or non-discretionary, outside the regular cycle.
• Severance or final pay owed outside the normal schedule. See Terminating an Employee.
• Retroactive pay to correct an underpaid period.
• PTO payouts and other one-time payments.
• A new hire who cannot wait for the next regular pay date.

When not to use it: a change that should apply to a run still in Draft (edit that run, or cancel and restart it), or a permanent profile change (Making Employee Payroll Updates).

Special vs Adjustment: which pay run type?

The start screen asks for a Pay Run Type: Special or Adjustment.

Before you select employees for an Adjustment run, UZIO reminds you: "Please ensure you have voided the original vouchers, if applicable, before selecting for adjustment to avoid double entries for the same pay period." In practice, the correction path for a wrong approved paycheck is: ask UZIO Support to void the original paycheck (see Payroll History), then re-enter the correct figures in an Adjustment run (data only) or a Special run (if money must also move).

Prerequisites

• Payroll setup is complete (the same requirements as a regular run).
• No conflicting payroll is in flight for the same employees. If one is initiated or approved for the same period, you will see: "You cannot add pay stubs because one or more payrolls have already been initiated or approved for this employee. Please reach out to support@uzio.com." Resolve that run first.

Steps

1. From the Payroll Dashboard, start a special payroll (the button reads Run Special Payroll, or Resume Special Payroll if one is in progress).
2. On the start screen, complete:
   • Pay Run Type: Special or Adjustment (see above).
   • Pay Group: the pay group of the employees you want to pay.
   • Pay Period start and end dates. Unlike a regular run, you choose the period. Any period is available.
   • Pay Date. Validated the same way as a regular run: weekends and federal bank holidays are not selectable. See Payroll Processing on Bank Holidays.
   • Apply Deductions (Yes/No) and Apply Contributions (Yes/No): whether the employees' standing deductions and employer contributions should be taken on this run. For a bonus-only run you usually choose No for both. For a skipped regular period you usually choose Yes for both.
3. Select the employees to include.
4. Enter earnings for each employee (bonuses, severance, PTO payouts, and other one-time payments). The grid toolbar includes the same Payroll Grid Tools as a regular run, plus a Gross-Up Net button available only on Special runs. See Grossing Up Net Pay.

Two grid behaviors to watch:

• The grid auto-populates each selected employee's hours and amounts from their profile(salary or hourly rate and standard hours). It does not know why you are running the special. Zero out any pre-filled amounts that do not belong, and enter only what you actually owe.
  • PTO hours can arrive automatically — check the grid before you enter them. For a terminated employee, the first payroll that runs after the termination picks up their PTO hours automatically, whether that run is regular or special, as long as the employee is included in it. Look at what is already in the grid before adding anything, so the same hours are not paid twice. Enter PTO hours yourself only where the grid has not filled them in. Zero-wage entries such as unpaid training hours revert to profile-based auto-population unless you re-enter them.

[Screenshot: special payroll grid with selected employees and one-time earning columns; use demo data]

1. Click Continue and review the summary: deductions, taxes, the Payroll Health Check findings, and the cost. Full tax and deduction calculations apply, the same as a regular run.
2. Approve. The same approval rules apply as a regular run: approval is final on your side, and direct deposit needs 2 business days between approval and the pay date. See Processing a Regular Payroll.

Expected outcome

• Employees receive payment via their normal payment method (direct deposit or check), subject to the same direct-deposit lead time as regular payroll.
• The special payroll appears in Payroll History and in reports alongside regular runs, with type Special (or Adjustment).
• Pay stubs are visible to included employees on the pay date.
• Wages and taxes from the run count toward year-to-date totals, quarterly returns, and the W-2 like any other paycheck.
• No confirmation email is sent for Special or Adjustment runs. Only Regular runs send one.

Still stuck?

If you cannot start a special payroll because another run is blocking it, or you are unsure whether a Special or an Adjustment run is the right correction, please reach out to us at support@uzio.com or call +1-571-601-1752. Include the affected employees, the pay period, what was paid or reported incorrectly, and the Payroll No of the original run if there is one.

Related articles

• Processing a Regular Payroll
• Reviewing Past Payrolls and Requesting a Void (Payroll History): void first, then adjust
• Understanding and Setting Up Pay Groups: why pay periods get skipped
• Grossing Up Net Pay: often used with bonus special payrolls
• Printing Employee and Contractor Checks: paying by check on a special run
• Terminating an Employee: final pay timing