A payroll audit is not just something you do when trouble arrives. It is how you catch small errors before they compound into penalties, disputes, or a stressful review. Run through this checklist periodically (a quarterly cadence works well) to keep your payroll defensible.
1. Computation accuracy
- Are you using the current SSS, PhilHealth, Pag-IBIG, and BIR tables? Outdated tables quietly produce wrong figures.
- Is the order of computation correct, statutory deductions before withholding tax?
- Do premiums (overtime, holiday, night differential) match actual attendance?
- Is 13th month pay based on basic salary earned, not gross?
2. Remittances and filing
- Do remittance amounts reconcile with what was deducted from payslips?
- Were all contributions and taxes filed and paid on time? Keep the proofs.
- Do monthly runs reconcile with year-end reports (BIR alphalist, Form 2316)?
3. Records and documentation
- Are payslips issued and retained for every run?
- Are timekeeping records complete and tied to the pay computed?
- Are payroll records retained for the required period? Confirm with DOLE and the BIR.
4. Deductions and consent
- Is every non-statutory deduction backed by the employee's written authorization?
- Are loan balances (SSS, Pag-IBIG, company) tracked to completion?
5. Controls
- Is there separation of duties between preparing, approving, and releasing payroll?
- Is access to pay rules and bank details restricted and logged?
Turn the audit into a routine, not a fire drill
Most of this checklist is easy when your data is already consistent and reconciled. A payroll system that keeps tables current, ties pay to attendance, and preserves an audit trail turns the quarterly audit into a quick review. BeavHR is built to keep those records clean the whole year. Book a demo to see how it holds up to scrutiny.
Related reading
- The Complete Guide to Philippine Payroll Compliance
- The Employer's Payroll Calendar
- 7 Payroll Mistakes Employers Make
Disclaimer: This article is general information, not legal or tax advice, and Philippine rules and rates change over time. Always confirm the current requirements with the relevant government agencies, DOLE, BIR, SSS, PhilHealth, Pag-IBIG, and the National Privacy Commission, or your legal counsel before acting. Last reviewed: July 2026.