Run Your First Pay Run

Last updated: 2026-06-06 Summary:

• Employees carry a pay type (hourly, daily, or salary) and a tax profile; the pay-run wizard does the rest.
• Statutory deductions — SSS, PhilHealth, Pag-IBIG, withholding tax — compute from the seeded tax tables, not numbers you type in.
• The 13th-month pay run is its own run type for Philippine companies, with the tax-exempt portion handled.

Payroll is available on plans that include it — see Pricing.

Set up employees

1. Go to Payroll → Employees and add each employee.
2. Set the pay type — hourly, daily, or salary — and the rate. Daily employees are paid days worked times the daily rate (no overtime multiplier); hourly employees add overtime at the ordinary-day premium; salaried employees get a fixed amount per period.
3. Complete the tax profile so withholding computes correctly.

The statutory tables themselves live under Payroll → Tax Tables, seeded per country. You don’t maintain rates by hand; check the tables against current government schedules with your accountant when in doubt.

Run a regular pay run

1. Go to Payroll → Pay Runs and create a new run.
2. Select the pay period.
3. Review each employee’s line — edit hours or amounts where the period demands it. For hourly and daily employees you can also Pull from timesheets to fill blank hours from approved weekly time. See Bring timesheet hours into a pay run.
4. Check the gross-to-net math: gross pay, then SSS, PhilHealth, Pag-IBIG, and withholding tax, down to net pay.
5. Approve, then process. Approving and processing are separate permissions — one person can sign off (approve) and another can commit the run to the books (process). The run posts salary expense, the statutory payables, and the withholding payable, all from the same numbers on the screen. See Pay-run statuses.

If a period’s deductions ever exceed an employee’s gross pay, net pay floors at ₱0 and the shortfall is carried as arrears onto the next regular run rather than posting a negative net — see How payroll is computed.

The 13th-month run (Philippines)

1. Create a pay run and choose the 13th Month type.
2. Select the tax year; eKapital computes each employee’s amount from their year-to-date basic salary, with a months-worked override for mid-year hires.
3. Review the tax treatment — the exempt portion and any taxable excess are split out for you.
4. Confirm and process, the same as a regular run.

Where people get tripped up

• Tax profile left incomplete. Withholding can’t compute right without it, and the error compounds every period until annualization. Finish the profile before the first run.
• Treating the payables as paid. Processing a run books what you owe SSS, PhilHealth, Pag-IBIG, and the BIR — remitting it is a separate step on each agency’s calendar. See the filing deadlines checklist for the BIR side.
• Forgetting the year-end paper. Each employee gets a Form 2316 after year end, generated from the same payroll records. See Issue BIR Form 2316 and BIR forms & templates.
• Looking for a payslip PDF. eKapital doesn’t produce a per-employee payslip PDF — use the payroll reports (Employee Earnings is the per-person view) for payroll figures.

See also

• Enter and approve weekly timesheets
• Bring timesheet hours into a pay run
• Pay-run statuses
• How payroll is computed
• Payroll reports
• Tax handling
• BIR compliance overview