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.
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.
4. Check the gross-to-net math: gross pay, then SSS, PhilHealth, Pag-IBIG, and withholding tax, down to net pay.
5. Confirm and process. The run posts to the books — salary expense, the statutory payables, and the withholding payable, all from the same numbers on the screen.

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 BIR forms & templates.

See also

• Tax handling
• BIR compliance overview