How long does it take to run payroll in Timekeep?

Once your employees and schedules are set up, generating a payroll takes a few minutes. You review the attendance, create the payroll, check the payslips, and finalize. Most owners finish in under 15 minutes per cutoff.

Do I need to enter each employee's deductions manually?

No. Timekeep computes SSS, PhilHealth, Pag-IBIG, and withholding tax automatically based on each employee's salary. The contributions are always based on the current government tables.

What happens if an employee had overtime or was late?

Late minutes, undertime, overtime, and night differential are all tracked from attendance and applied to the payslip automatically. You can review each item before finalizing.

Can I run payroll for part of my team and finalize later?

Yes. You can generate payslips, review them, and only finalize when you're ready. Draft payslips are not visible to employees until you finalize the payroll.

What does finalizing payroll do?

Finalizing locks the payslips and makes them visible to employees in the portal. It also records the payroll as complete. You can still view the details after finalizing.

How to run payroll in Timekeep from start to finish

Cutoff day used to mean clearing the afternoon. Opening the biometrics file, matching it to the schedule, noting who was late, who had overtime, who was absent. Pulling up the SSS table to compute contributions. Running the numbers in a spreadsheet, double-checking, and then starting the payslips one by one. Then screenshotting and sending them out on the group chat.

If that sounds familiar, here's what the same day looks like in Timekeep. You open the payroll page, create a new payroll for the cutoff period, review the generated payslips, and finalize. Your team sees their payslips in the portal.

This walkthrough covers the full process from start to finish.

What Timekeep needs before you can run payroll

Before you run your first payroll, three things need to be set up: your employees, their work schedules, and the payroll settings for your business.

Employee records need a daily or hourly rate, or a fixed salary, and the hire date. For government deductions to compute correctly, each employee's SSS, PhilHealth, Pag-IBIG, and BIR numbers should be on file, though payroll will still run without them.

Work schedules tell Timekeep when each person is supposed to start and end. Without a schedule, Timekeep can't flag late arrivals or compute overtime against the shift end time.

Payroll settings let you configure your pay frequency (semi-monthly or monthly) and which government contributions to include. You only set these once. When creating a payroll, you choose 1st or 2nd cutoff and the date range for the period.

Step 1: Review attendance before running payroll

Before creating a payroll, check the attendance records for the cutoff period. Go to Attendance in the dashboard and filter by the date range of your cutoff.

Look for any incomplete records. An incomplete record means someone clocked in but never clocked out, which usually means a forgotten clock-out. You can manually set a clock-out time for those records before running payroll.

Timekeep attendance dashboard showing clock-in and clock-out records

You can also see late minutes, overtime hours, and any flagged attendance issues here. These are the numbers that will flow into the payslips.

Step 2: Create a new payroll

Go to Payroll and click New Payroll. Choose 1st or 2nd cutoff, then set the start and end dates for the period. Timekeep will pull all attendance records for that date range and generate payslips for every active employee.

Timekeep new payroll dialog showing cutoff selection and date range

Generating a payroll takes a few seconds. When it's done, you'll see a list of payslips, one per employee.

Step 3: Review each payslip

Click on any payslip to see the full breakdown. The payslip shows:

Basic pay for the period based on the rate and days or hours worked
Holiday pay for any regular or special non-working days in the period
Overtime pay if any overtime was approved
Night differential for hours worked between 10 PM and 6 AM
Deductions for late minutes and undertime
Government contributions: SSS (employee share), PhilHealth, Pag-IBIG, withholding tax
Any loan deductions

Timekeep payslip showing full earnings and deductions breakdown

Everything is itemized. If a number looks off, you can trace it back to the attendance record or the rate setting. Timekeep doesn't hide anything.

Step 4: Check the payroll summary

Back on the payroll detail page, you can see all payslips at a glance. The summary shows total gross pay, total deductions, and net pay across all employees.

Timekeep payroll detail showing all payslips for a cutoff period

If anything needs adjustment, you can edit an employee's attendance record, recompute the payslip, and review again before finalizing.

Step 5: Finalize the payroll

When everything looks right, finalize the payroll. This locks the payslips and makes them visible to your team in the employee portal. Employees can view and download their payslips from their phone without texting you.

Finalized payrolls stay in your payroll history. You can go back and view any payslip from any period.

What gets computed automatically

Every payroll run computes the following without any manual input from you:

SSS contributions. Timekeep looks up the correct Monthly Salary Credit based on the employee's gross pay and computes the employee share and employer share. It also handles the Mandatory Provident Fund for employees earning above ₱20,000.

PhilHealth. Computed at 5% of the monthly basic salary, split between employee and employer, using the current salary floors and caps.

Pag-IBIG. ₱200 flat for most employees, matched by the employer.

Withholding tax. Computed based on the TRAIN Law brackets for the employee's annual taxable income, taking into account government contributions deducted before tax.

Holiday pay. Any holidays in the cutoff period are applied automatically. Regular holidays use a 200% multiplier for worked hours. Special non-working days use 130%. Rest day premiums stack on top.

Overtime. Approved overtime hours are computed at 125% of the hourly rate for regular days, with higher multipliers for holidays and rest days.

After payroll: what your team sees

Once you finalize, every employee can open their payslip in the portal. The portal is a website your team opens on their phone. They log in with a 6-digit PIN and see their payslips, past and present.

No group chat, no screenshots, no PDFs sent over Viber. They check it themselves.

Try it free for 30 days at timekeep.ph.