Run a Payroll

Purpose

This guide walks you through processing one payroll cutoff end to end, from creating the pay run to generating approved payslips. Follow it every time you prepare pay for a period.

Before you start

• Confirm attendance for the cutoff is finalized, including overtime, holidays, night differential, and approved leaves.
• Confirm employee salary history and earning and deduction templates are current.
• Confirm any commissions and payroll adjustments for the period are recorded and approved.
• You need the Create Payroll permission to add a run and Payroll Manager rights (or be the assigned signatory) to process it.

Procedure

1. Open the pay runs list. Go to Compensation > Payrolls.

2. Create the pay run. Click Add, then set the pay period start and end dates, the account, the department or coverage, and a title. Save. The new run appears with a Draft status.

3. Set the payroll options. From the run's actions menu, choose Set Options and confirm the tax table, pay rates, contribution handling, and inclusions for this cutoff. This controls how pay is computed.

4. Initialize the run. From the actions menu, click Initialize. The status changes to Ongoing, which locks the run's setup and prepares it for processing. A Draft run can still be edited or deleted before this step.

5. Open the run. On an Ongoing run, click the payroll to open its run page. Validate checks the run before you process it — it works through the employees in batches and reports each one in the activity console, so a large payroll shows steady progress rather than appearing to hang. The run panel lists the processing steps; Run step performs the current one for every payslip, and Auto-run works through the steps in order without stopping. Either way each payslip is built for an included employee, with gross pay, statutory deductions, taxes and net pay computed from the attendance and compensation data.

   Processing runs in batches and reports progress in the activity console beneath the panel, naming each batch and every failure. You can close the browser and come back: the run is tracked server-side, so reopening the page shows where it got to and offers to resume.

   Auto-run finishes at Compute and stops there. It works through attendance, earnings, deductions and any optional components the payroll includes, then runs Compute, which freezes each payslip's net pay. Review and Approve stay manual on purpose — approving a payslip signs it with your name, so it is never something an unattended run does for you.

   Because Compute freezes the payslips, a second Auto-run over the same payroll will not recompute anything — every step declines a payslip that is no longer a draft, and the run ends saying so rather than reporting success. If you correct a timesheet, a commission or an adjustment after computing, set the affected payslips back to Draft first (payslip menu → Mark as draft), then run again.

6. Work through each employee. Review the computed figures. Where a rate changed mid-cutoff, the engine applies the correct rate per day. Use Investigate on a payslip to see the detailed breakdown behind any number.

7. Resolve exceptions. The Checks column flags each employee as Ready, Review or Blocked, and its tooltip names every signal that fired. The Exceptions tab turns those findings into a searchable employee list: one row per person, with their ID number, name, job title and department, and a Findings column naming everything wrong with them — missing salary record, missing attendance, missing schedule, or zero/negative net pay. The four buttons above the table carry the count for each finding and filter the list to it, so "12 employee(s) have no salary records" becomes the twelve names. The vs previous column on the payslip grid shows how each net pay moved against the last payroll, which is the fastest way to spot a figure that has changed unexpectedly. Correct the source data for anything flagged, then recompute that payslip.

8. Approve the payslips. Move each reviewed payslip from Pending to Approved. Only approved payslips are ready for release.

9. Complete the run. Once all payslips are approved and checked, finalize the payroll so its status becomes Completed. You can then view the payroll summary and distribute payslips.

Expected result

The pay run shows Completed, every included employee has an Approved payslip with correct net pay, and the payroll can be viewed, exported, and posted for payment. Government contributions and taxes are captured for later BIR reporting.

Troubleshooting

• An employee has no pay or a zero rate. Check that their salary history has an approved current rate, then recompute the payslip.
• Hours or overtime look wrong. Return to Attendance, finalize the cutoff, then re-run the affected step from the run panel.
• You cannot edit the run. Only Draft runs are editable. An Ongoing or Completed run must be cancelled first if setup was wrong.
• A figure looks off. Open the payslip's Investigate view to trace how it was computed before making changes.