Payroll Checklist for Every Cutoff in the Philippines

Payroll errors usually begin before anyone calculates net pay. A missing clock-out becomes a short day. An approved overtime request stays in chat. A rate change reaches the spreadsheet after the draft is finished. The safest response is not a longer formula. It is a repeatable process that makes incomplete inputs visible before payday.

This payroll cutoff checklist is for the owner, HR lead, payroll processor, or bookkeeper responsible for each regular pay cycle. Use it in the same before, during, and after order every time. If you are still designing your schedule, start with how to set up payroll cutoffs and paydays.

The legal baseline matters. DOLE's FAQs on wage and wage-related benefits state that wages should be distributed once every two weeks or twice a month, at intervals not exceeding 16 days. The same guide covers holiday, rest-day, overtime, and night-work premiums for covered employees. Your exact treatment can still depend on employee coverage, the applicable wage order, contracts, and company policy.

Before payroll: freeze the scope and close the inputs

1. Confirm the period, payday, people, and changes

Write the payroll header before working on any employee:

• Period start and end: Use the work dates included in this run, not the date you happen to process it.
• Payday: Confirm the bank or cash-release date and leave enough time for review and funding.
• Included employees: Start from the active roster, then account for new hires, resignations, transfers, unpaid periods, and anyone intentionally handled in another run.
• Approved pay changes: List changes to rates, compensation type, allowances, recurring deductions, loan schedules, and payroll eligibility, with their effective dates.

Compare the list with the previous cutoff. An unexpected addition or removal is a review item, not something to ignore. Keep evidence of who approved each change and when it takes effect. A correct new rate applied to the wrong period is still wrong payroll.

Timekeep supports configurable semi-monthly periods and paydays, selected employees, and saved employee groups. The selection remains specific to that payroll run, so you can verify exactly who is included instead of assuming the whole roster is unchanged.

2. Close attendance, leave, overtime, and calendar exceptions

Review the whole period by employee and work date. Resolve:

• incomplete clock-ins, clock-outs, and breaks;
• missing logs and duplicate attendance;
• approved paid or unpaid leave;
• late, undertime, and absence treatment;
• overtime approval and the actual approved minutes;
• scheduled rest days and work performed on them;
• regular and special holidays in the employee's work location; and
• overnight work assigned to the correct work date.

Do not fill a gap from memory. Ask for a correction, approval, schedule, or other source record. This preserves a trail when an employee later asks why a day was paid a certain way. Use the detailed attendance clean-up guide when records do not line up.

In Timekeep, payroll generation blocks when selected employees have incomplete attendance that can affect pay. That stop is useful, but it is not a substitute for reviewing approved overtime, leave, rest days, holidays, and suspicious but technically complete logs.

Stop payroll if…

• the period, payday, or employee list is still disputed;
• a pay-relevant attendance record is incomplete or unsupported;
• an approved rate or earnings change has no clear effective date;
• overtime, leave, rest-day work, or holiday treatment is unresolved;
• statutory deduction timing cannot be confirmed; or
• the draft contains a duplicate, an unexplained negative net pay, or a material total that nobody can explain.

Fix the source record, document the decision, and regenerate the draft. Do not lock a run merely because the payment deadline is close.

During payroll: calculate, draft, and challenge the result

3. Check every earnings and deduction category

For each employee, move from gross pay to net pay in a fixed order.

Base pay. Confirm the compensation type and effective rate. Check the paid days, hours, or semi-monthly amount against the closed period.

Premiums. Review holiday pay, rest-day premium, overtime, and night shift differential against the dates and approved work. DOLE's wage FAQs are a useful starting point, but use the current official rule that applies to the employee and day.

Allowances and extra earnings. Check whether each allowance is fixed, attendance-based, taxable, exempt, or scheduled for a particular cutoff. Add approved commissions, incentives, reimbursements, or other extra earnings only once and label them clearly.

Deductions and loans. Confirm recurring deductions, cash advances, loan amortisations, attendance deductions, and any one-off adjustment. Each amount needs a lawful or authorised basis and should not be copied blindly from the prior run.

Contributions and withholding tax. Confirm whether SSS, PhilHealth, Pag-IBIG, and BIR withholding belong in this cutoff under your configured timing. Check employee identifiers, eligibility, compensation basis, and whether the amount was already taken in another cutoff. Use current official guidance rather than a saved table:

• The BIR withholding tax page and its official calculator cover payroll-period withholding on compensation.
• The SSS employer guide requires employers to deduct the employee share, add the employer share, remit them, and maintain accurate payroll and deduction records.
• PhilHealth's employer guide says employers must remit employee premiums and counterpart shares correctly, on time, and with accurate reporting.
• Pag-IBIG's official implementing rules for RA 9679 cover employer deduction, counterpart contributions, remittance, and records.

Those obligations are generally monthly even when wages are paid semi-monthly. This checklist only confirms that the correct amount is captured in the correct cutoff. Actual agency reporting and remittance happen in the later compliance workflow.

Timekeep can calculate contributions and withholding tax, apply configured contribution timing, and include loans, recurring deductions, allowances, and manual payslip adjustments. The processor still owns the inputs and review.

4. Generate a draft and test the worst errors first

Generate the payroll as a draft. Then review the summary and individual payslips before approval. Start with the errors that are most embarrassing and costly:

1. Wrong employee: Is someone missing, duplicated, inactive, or included in the wrong group?
2. Wrong date: Does every attendance, leave, holiday, loan start, and pay change belong inside this period?
3. Wrong rate: Does the draft use the approved compensation rate effective for these dates?
4. Duplicate item: Did an allowance, overtime entry, deduction, loan, or correction appear twice?
5. Missing approved work: Is approved overtime, rest-day work, holiday work, or paid leave absent?
6. Unexplained net pay: Can the reviewer explain the movement from gross pay to net pay, especially large changes, zero pay, or a negative amount?

Use comparisons, not only spot checks. Compare headcount and total gross, deductions, and net pay with the previous cutoff, then explain material differences. Compare each unusually high or low payslip with its attendance and changes. Recalculate a small sample independently, including at least one employee with overtime or a deduction.

If a source input changes, regenerate the affected draft and repeat the checks. Timekeep supports full draft regeneration and individual payslip regeneration, with manual extra earnings and custom deductions available while payslips are unpaid. The step-by-step Timekeep payroll guide shows the product workflow.

5. Approve or lock, pay employees, and issue payslips

The approver should review the final draft, the exception notes, and the payroll totals. Record who approved it and when. Lock the run only after open questions are resolved.

Next, fund and release wages through your chosen payment channel. Match the payment file or instruction to the approved net-pay list before sending it. Confirm failed or returned payments separately; a locked payroll record does not prove that money reached an employee.

Issue an itemised payslip for the pay period so each employee can see earnings, deductions, and net pay. SSS's implementing rules specifically require a receipt for deducted SSS contributions or that the deductions appear on the employee's payslip or pay envelope.

Timekeep uses a draft → locked → paid lifecycle. Locked and paid payslips are available in the employee portal; dashboard users can generate individual payslip PDFs or a batch ZIP. Marking a locked run paid preserves the paid record and applies generated loan payments. Timekeep does not send the bank transfer, so keep payment confirmation with the run.

After payroll: preserve evidence and hand off totals

6. Save reports, corrections, and accounting totals

Close the cutoff by saving one complete evidence set:

• approved payroll summary and per-employee detail;
• issued payslips or generated PDFs;
• payment proof, bank reference, or signed cash payroll record;
• final attendance and leave source records;
• approvals for overtime, rate changes, earnings, and deductions; and
• a correction log showing the issue, affected employee and period, amount, approver, and how it will be resolved.

Do not silently overwrite an error after payment. Record whether the correction was paid separately or will appear as a clearly labelled adjustment in a later cutoff. Tell the affected employee what changed.

Give accounting or the bookkeeper the approved totals for gross pay, each earning category, employee deductions, employer contributions and labour cost, and net pay, together with payment proof. Timekeep provides per-run CSV exports, individual PDFs, batch payslip PDFs, and paid payroll history. See how to export payroll reports for accounting.

The handoff should also identify totals that will feed later BIR, SSS, PhilHealth, Pag-IBIG, and loan-remittance work. Stop there. Monthly reconciliation, accounting close, agency filing, 13th-month pay, and year-end work belong in separate procedures, not this every-cutoff checklist.

Copyable payroll processing checklist

BEFORE
[ ] Confirm period start/end and payday
[ ] Confirm included employees, new hires, exits, and exclusions
[ ] Confirm approved rates, allowances, deductions, and effective dates
[ ] Close attendance, breaks, leave, overtime, and missing logs
[ ] Check schedules, rest days, holidays, and overnight work dates

DURING
[ ] Check base pay and paid days/hours
[ ] Check OT, holiday, rest-day, and night premiums
[ ] Check allowances and extra earnings once each
[ ] Check deductions, loans, and contribution timing
[ ] Check SSS, PhilHealth, Pag-IBIG, and BIR inputs
[ ] Generate draft and compare headcount and totals
[ ] Test wrong employee, date, rate, duplicates, and missing approved work
[ ] Explain every unusual, zero, or negative net pay
[ ] Approve/lock the final run
[ ] Pay employees and confirm failed payments
[ ] Issue itemised payslips

AFTER
[ ] Save final reports, payslips, approvals, and payment proof
[ ] Record corrections; never silently overwrite paid payroll
[ ] Hand gross, deductions, employer costs, and net totals to accounting
[ ] Flag totals for later tax, contribution, and loan remittance work

Make the same checks easier next cutoff

A checklist works best when it is short enough to use and strict enough to stop a bad run. Keep one owner for each input, one approver for the final result, and one saved evidence set for every cutoff.

Timekeep brings attendance, payroll inputs, draft review, payslips, exports, and paid records into one workflow for Philippine small businesses. Explore Timekeep payroll if you want to run this checklist with fewer spreadsheet handoffs.

This article provides general operational guidance, not legal, tax, or accounting advice. Rules can vary by employee coverage and business circumstances. Check current DOLE, BIR, SSS, PhilHealth, and Pag-IBIG guidance, and consult a qualified adviser for your situation.