Expertise

VAT Compliance & Refund Claims

Document-led counsel for BIR notices, assessments and corporate tax risk.

VAT positions should follow the transaction and the record.

NLF reviews VAT classification, invoicing, disputed positions and refund procedure with the client’s finance team. The first task is to identify the transaction, period and statutory route, not to assume that every input credit is refundable.

Illustrative tax-review folders and unbranded records

Governing VAT authorities

Registration, invoices and returns

Registration depends on taxable activity, applicable thresholds and mandatory or voluntary coverage. VAT-registered taxpayers ordinarily file quarterly VAT returns from January 2023. Do not treat optional or special arrangements as a universal monthly-return obligation.

EOPT makes invoices the principal sales documents for goods and services. Review actual invoice requirements and the applicable transition, rather than relying on an old official-receipt checklist. For systems changes, see electronic invoicing.

Zero-rating is transaction-specific

Zero-rated sales and VAT-exempt sales are different. Export or investment registration alone does not establish zero-rating for every sale or purchase. Review the statutory category, project registration, attribution, certifications, customer and use of the goods or services.

A refund requires eligible, substantiated input VAT and proof that it has not already been applied or recovered. Cross-border services also require digital VAT and reverse-charge analysis where relevant.

The current refund decision path

TRAIN shortened the VAT processing period to 90 days; EOPT did not introduce that change. CREATE MORE subsequently amended the denial route. For claims covered by RR Nos. 8-2025 and 10-2025, including the applicable April 1, 2025 implementation transition, use the following sequence. Older claims require the rules applicable to their filing and events.

Covered VAT refund procedural events
Event	Period	Action
Complete claim	90 days from submission of certified true copies of invoices and other supporting documents	Record the accepted submission and required-document checklist.
Full or partial denial	15 days from receipt	Request administrative reconsideration. Failure to do so makes the denial final under the amended provision.
Reconsideration filed	15 days from receipt by the BIR	The BIR must decide the request. The implementing rules limit the grounds and supporting material.
CTA review	30 days from the applicable denial or lapse	Distinguish denial of reconsideration, original 90-day inaction and 15-day reconsideration inaction. Do not wait indefinitely.

A request for reconsideration is not an opportunity to repair an incomplete original file by submitting previously omitted mandatory documents. Continued administrative processing should not be assumed to stop a judicial appeal deadline.

For qualifying Section 112(A) claims, the administrative filing period is two years from the close of the taxable quarter of the relevant sales. Registration cancellation has its own Section 112(B) trigger. See the claim-type guide before applying a deadline. Historical San Roque discussions of the former 120-day regime do not state the current timetable.

What the review can produce

VAT legal work and finance coordination
Issue	Potential scoped output
Classification	Written analysis of taxable, exempt or zero-rated treatment.
Records	Legal substantiation checklist and reconciliation questions for finance.
Refund	Claim strategy, document review and procedural calendar.
Dispute	Response, reconsideration or CTA strategy under a separate agreed scope.

Routine bookkeeping, return preparation, audit work and litigation are not automatically included in an initial legal review. Responsibilities and scope are agreed expressly.

Questions about timing and recovery

Does the BIR always resolve a refund within ninety days?

The law provides a processing period with defined triggers and remedies for inaction. It does not guarantee payment within that time. Avoid assuming continued processing extends the CTA deadline.

Is every PEZA-related purchase zero-rated?

No. The current law, registered project, transaction, attribution and supporting requirements must be met.

What should I send initially?

Identify the taxpayer, tax period, claim type and latest BIR document or receipt date. Detailed records can be requested after conflict and scope screening.

Discuss Your Matter

Provide only high-level information reasonably necessary for conflict and scope screening. Engagement is subject to conflict checking and written acceptance.

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