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Run your first payroll
Create a payroll run, check the payslips, lock it, and mark it paid.
Before you start
A payroll run only reads what is already in Timekeep, so it is worth checking these four things first.
- Everyone you are paying has a pay rate on their record in Staff.
- Schedules cover the dates you are paying for. Pay is measured against the schedule.
- Attendance for those dates has been reviewed in Attendance. Set the date range, then set the status filter to Incomplete to see the days that still need work. Follow Correct an attendance record for a missing punch.
- Approved leave is recorded in Leaves. Overtime is approved with Approve OT in the same actions menu.
Steps
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Go to Payroll and click New Payroll.
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Choose the Period, either Semi-monthly or Weekly.
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For semi-monthly, choose the Cutoff, either 1st Cutoff or 2nd Cutoff. Start Date and End Date then fill in for you, and they are the attendance dates the run covers. For weekly, Start Date must be the first day of your payroll week, and End Date is locked to six days later.
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Set the Payout Date, the day your staff actually get paid. Timekeep needs it before it can create the run. It is not an attendance date, so it often falls in the next month.
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Choose who is included. Employee group starts at All active employees. Pick a saved group instead, or tick names in the list on the right. Save this selection as a new group keeps the same set of people for next time.
The New Payroll dialog. Attendance dates are on the left with the Payout Date below them, and the employee list is on the right. -
Click the create button. It counts your selection, so it reads like Create Payroll for 12 Employees.
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Click Run Payroll. This is the step that builds the payslips. If the Incomplete attendance found dialog appears, click Review attendance, fix the records with no clock-out, then come back and run it again.
A draft payroll run. Run Payroll, Lock and Download All sit above Payroll Entries. -
Check the payslips while you still can change them. Payroll Entries lists everyone with Gross Pay, Additions, Deductions and Net Pay. Click a row to open a payslip. In Pay Breakdown, Earnings add up to Gross Pay. Deductions then holds the SSS, PhilHealth and Pag-IBIG contributions, Withholding Tax, and any late, undertime, overbreak or absent amounts. If a figure surprises you, View Calculation opens the full calculation breakdown for the payslip. Add Earning and Add Deduction cover one-off items such as a ₱2,000 bonus or a ₱500 cash advance.
A payslip, with Earnings on the left and Deductions on the right. -
If a figure is wrong, fix the record it came from, whether that is the attendance, the leave, the rate or the loan. Then click Run Payroll again while the run is still Draft. The rerun rebuilds every payslip from the source records. It keeps the Additional Earnings and Additional Deductions you typed, so they still count in net pay.
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When the figures are right, click Lock. Then click Mark as Paid, tick I have reviewed all payslips and confirm this payroll is correct, and click Confirm.
What happens next
A run moves through three states, and each one allows fewer changes than the one before.
- Draft. You can run it, rerun it, edit payslips, and delete the run.
- Locked. Run Payroll is off, so payslips are not rebuilt from attendance. Unlock puts it back to draft. Your staff can now see their payslip.
- Paid. The run is final. Loan payments are recorded, loan balances go down, and every payslip is stamped as paid. A paid run cannot be unlocked.
To download, click Download All and pick PDF (ZIP) or CSV. A single payslip has its own Download PDF button.
Employees see the payslip on the Payslips page of the portal as soon as the run is locked. They do not wait for it to be marked paid.
Common problems
- Run Payroll stops with a dialog. Someone in the run has attendance with no clock-out. Those records are left out of pay, so fix them before you run it.
- Someone is missing from the New Payroll list. It is usually the pay frequency. A weekly run lists only daily and hourly staff on weekly pay, and a semi-monthly run leaves out anyone on weekly pay. Deactivated staff never appear.
- Mark as Paid is not there. The run is still a draft, so click Lock first.
- A change is needed after paying. A paid run cannot be unlocked, so correct it in the next run.
Share Log in to the employee portal and View your payslips with your staff so they can find their payslips.
Last updated Sep 20, 2026