BIR Tax Audits in the Philippines Made Simple: A Proactive Guide for Business Owners
By: Noel C Ducusin
If your business is operating in the Philippines and you receive a notice from the Bureau of Internal Revenue (BIR) for a tax audit, don't panic. This routine process typically happens within the first three years of your business operations. The reason for this timing is that the BIR’s right to collect taxes generally expires after three years. As a result, tax audits are a regular matter and should not automatically be seen as a sign of wrongdoing.
By understanding the audit process and planning with your accountant, you can navigate it smoothly and even use it as an opportunity to improve your tax compliance. Here is a step-by-step guide to what you can expect and how to manage the situation effectively.
The BIR Tax Audit Process
While the audit process involves many details, here is a bird's-eye view of the key steps. This is all you really need to know to manage the process effectively while delegating most of the details to your accountant:
1. Issuance of Letter of Authority LA - The BIR issues a Letter of Authority, which authorizes a Revenue Officer to audit your company's records.
2. Service of LA - The LA is officially delivered to you as the taxpayer.
3. Audit Period - The Revenue Officer reviews your financial records, tax returns, and supporting documents.
4. Issuance of Preliminary Assessment Notice PAN - If discrepancies are found, the BIR sends a PAN detailing their findings and the proposed tax assessment.
5. Response to PAN - You have the opportunity to reply to the PAN and present your counterarguments.
6. Issuance of Final Assessment Notice FAN - If your response is not accepted or no response is submitted, the BIR issues a FAN stating the final tax assessment.
7. Formal Demand for Payment FD - If the tax liability remains unsettled, a Formal Demand for payment is issued.
What If You Disagree - The Appeals Process
If you do not agree with the BIR's assessment, there is a structured process to contest it:
1. File a Protest - Submit a written protest to the BIR Regional Director or the Commissioner of Internal Revenue.
2. BIR Review - The BIR will reassess the case and may conduct a reinvestigation.
3. BIR Decision - The BIR will issue a decision based on the review.
4. Appeal to the Court of Tax Appeals CTA - If the decision is unfavorable, you can appeal to the CTA.
5. Further Appeals - If necessary, further appeals can be made to the Court of Appeals and even the Supreme Court.
Cost Management
You don't need a lawyer until you reach the CTA level, allowing you to minimize legal costs during the initial protest phase.
The BIR often rules in its favor, meaning court intervention may be necessary to reverse the decision.
When appealing, you are only required to pay the undisputed portion of the tax assessment and not the full amount.
Common Audit Pitfalls
There are some common mistakes that the BIR does that can lead to higher tax assessments. Identifying and addressing them early can save you money:
1. Double Recording of Taxes
The BIR uses separate systems for income tax TRS - Tax Reconciliation System and VAT RELIEF - Reporting of Exempt and Incentive-Filled Transactions. Because these systems are independent of each other, issues like double recording of revenue or expenses can occur. It is not just a matter of imperfect synchronization; there are inherent risks when different tax systems operate separately. Review your records carefully with your accountant to catch and correct these errors.
2. Unverified Income Allegations
The BIR often relies on computer records from your customers' databases or tax filings to identify undeclared income. However, these records alone are not proof of actual income unless supported by commercial invoices or certificates. If the BIR's assessment is based solely on these digital records, you can dispute it for lack of proper documentation.
Managing Cash Flow
A tax assessment doesn't mean an immediate full payment. By understanding the audit timeline, you can plan your cash flow more effectively:
You are not required to pay anything until after the Formal Demand FD is issued and you have filed a protest. This means you have time to prepare financially before making any payments.
You only need to pay the undisputed amount while appealing, allowing you to defer the disputed portion. The audit process provides an early indication of potential tax liabilities, helping you plan ahead.
Over time, as you become more familiar with the process, you can delegate more of the work to your accountant and focus on running your business.
Final Thoughts
With familiarity comes less stress. Once you understand the audit process, it becomes much easier to handle. Instead of feeling overwhelmed, you will know what to expect, how to respond, and when to prepare payments.
More importantly, this knowledge allows you to confidently delegate most of the work to your accountant.
About the Author
Atty. Noel C. Ducusin is the Director for M&A at DoingBusinessPH, where he works with offshore investors—primarily from Japan, Europe, the US, and Southeast Asia—seeking to enter the Philippine market through acquisitions, joint ventures, and strategic partnerships. He also advises local companies, family offices, and high-net-worth individuals on originating and executing transactions, including preparing businesses to be investment-ready through reverse due diligence.
His work spans the full M&A cycle: identifying counterparties, managing due diligence, leading negotiations, structuring transactions, arranging financing, and coordinating with trusted vendors such as banks, suppliers, and contractors. For startups and new ventures, he helps design fundraising-ready structures and connects them with investors, making DoingBusinessPH a natural bridge between global capital and local opportunity.
Beyond transactions, Noel and his team provide executive education and professional development through speaking events, seminars, and small-group sessions like business lunches and roundtables, then carry that value forward into practical, business-ready solutions. These include annual subscriptions for legal and regulatory updates, customized in-house corporate training, and post-event compliance audits, along with exclusive deep-dive masterclasses and peer mastermind groups for executives. They also prepare executive toolkits with ready-to-use templates and offer premium one-on-one consulting sessions—all designed to turn the insights gained from these settings into clear, actionable steps that help investors and businesses navigate the Philippine market with confidence.
A lawyer by training with a degree in Business Management, Noel is also Senior Partner at N. Ducusin & Partners Law Offices, which specializes in Mergers & Acquisitions, Investments, Cross-Border Regulatory, and Corporate Advisory. Over the years, he has developed deep, practical expertise in corporate finance, company valuation, and financial modeling through hands-on involvement as part of the deal team in live transactions. This combination of legal and financial experience allows him to bridge both perspectives seamlessly, ensuring that deals are not only executed but positioned for long-term success.
He is always looking forward to comparing notes with investors, startups, and vendors to explore where his clients’ mandates align with theirs and to uncover potential opportunities and collaborations that benefit both sides. Please feel free to connect with him to continue the conversation and explore where your goals and his clients’ interests may intersect.
His mission for this blog is to help foreign investors, business owners, and managers by breaking down complex legal concepts and dense technical material into simple, straightforward, and actionable insights for better business decisions. Articles and briefs are written in plain everyday language, without jargon or unnecessary academic writing—the simpler and more practical, the better.
“Everything should be made as simple as possible, but no simpler.” – Albert Einstein