Here’s a Philippine-focused, practice-oriented explainer on VAT registration for livestock sellers when gross sales/receipts exceed ₱3,000,000—with the key “ifs,” edge cases, computations, and compliance steps you’ll actually use.

Big picture (the decision tree)

What are you selling?
- Agricultural food products in their “original state” (e.g., live swine, cattle, goats, poultry; and typically carcasses/cuts that have only undergone simple prep/preservation and remain food): VAT-EXEMPT by nature.
- Non-food or not of a kind generally used for human consumption (e.g., fighting cocks, game birds, pets, race horses), processed meats beyond “original state,” hides, leather, rendered fats, etc.: VAT-TAXABLE goods (standard 12% output VAT) unless another specific exemption applies.
What did you exceed ₱3 million with—exempt or taxable sales?
- Exclusively VAT-exempt sales (original-state food livestock): You do not become VAT-liable or VAT-registered just because you crossed ₱3M. You remain non-VAT (but still BIR-registered as a taxpayer).
- Taxable sales (in whole or in part): Once your gross annual taxable sales/receipts exceed ₱3,000,000, VAT registration is compulsory and you must charge/collect VAT going forward.
- Mixed seller (some exempt, some taxable): Track two buckets. If the taxable bucket pushes you over ₱3M (combined taxable + exempt for the annual threshold test), you must VAT-register; after that, you still do not impose VAT on the exempt line but must on the taxable line.

Practical rule of thumb: Crossing ₱3M forces VAT-registration only if you are not exclusively engaged in VAT-exempt transactions. The ₱3M threshold is the “small-taxpayer” limit for taxable persons.

What “original state” means for livestock sellers

“Agricultural and marine food products in their original state” are VAT-exempt. For livestock, this means animals of a kind generally used as, or yielding/producing, food for human consumption (e.g., pigs, cattle, goats, sheep, chickens, ducks).
Simple preparation/preservation that doesn’t change the product’s essential character as food (e.g., chilling, freezing, basic cutting, dressing) typically remains within “original state.”
Outside original state: products primarily for sport, show, or not generally for human consumption (e.g., fighting cocks), and processed products with transformation beyond simple prep (e.g., sausages, ham, canned meats) → VAT-taxable.

If your catalog includes both (say, live hogs and value-added meat products), you’re a mixed seller: part exempt, part taxable.

Registration outcomes by seller type

A) Exclusively original-state livestock (food) seller

VAT status: Exempt regardless of volume (even well above ₱3M).
VAT registration: Not required (and in practice, not allowed if you are exclusively VAT-exempt).
Invoicing: Issue Non-VAT Sales Invoice/OR showing “VAT-Exempt Sale”; no output VAT.
Input VAT: Any VAT you pay on supplies/services becomes part of cost/expense (not creditable).
Other taxes: You’re generally not subject to the small-taxpayer percentage tax on those exempt sales. (You still have standard income tax, withholding, and bookkeeping duties.)

B) Mixed seller (original-state livestock + taxable products/services)

Threshold test: If your aggregate annual gross sales/receipts exceed ₱3M, you must VAT-register.
Post-registration:
- VAT-taxable lines: Charge 12% VAT; file VAT returns.
- VAT-exempt lines (original-state livestock): Still no VAT; separately invoiced as “VAT-Exempt.”
- Input VAT allocation: You must apportion input VAT between taxable and exempt activities (only the taxable portion is creditable).
Pre-registration excess: Once you cross the threshold, you’re deemed liable to update registration promptly; failure triggers assessed output VAT (prices deemed VAT-inclusive) plus penalties/interest.

C) Exclusively taxable livestock activities (e.g., fighting cocks, processed meats)

VAT registration becomes mandatory upon exceeding ₱3M.
Below ₱3M: You may remain non-VAT (small taxpayer) or opt to voluntarily VAT-register (binding for at least 3 years).
After crossing ₱3M: Start charging 12% VAT and filing monthly/quarterly returns; failure to update → assessments and penalties.

Timing: when “exceeding ₱3M” bites

The ₱3M is an annual threshold. If at any time within the year it becomes reasonably apparent you’ll exceed ₱3M (or you actually exceed it), update to VAT immediately (practically, within the next month).
Late registration: BIR can assess you for output VAT on taxable sales made after you should have been VAT-registered. If you billed without VAT, your prices are deemed VAT-inclusive (compute Output VAT = Gross/1.12 × 12%), plus surcharge (25% or 50% if willful) and interest (per current NIRC rates).
On registration, you may claim transitional input tax on beginning inventories (subject to NIRC/BIR rules and proper invoices) and regular input VAT on purchases going forward.

Invoicing & bookkeeping—what changes at VAT registration

Change your receipts: Use VAT Sales Invoice/Official Receipt for taxable sales, and continue issuing Non-VAT/Exempt documents for exempt sales (or a VAT invoice that clearly segregates a VAT-Exempt line at 0 output).
Segregate lines: Show separate totals for VAT-taxable, VAT-exempt, zero-rated (if any), and VAT amount.
Books of accounts: Keep books that allow clear separation of exempt vs taxable revenue and related costs for input VAT allocation.

Common livestock scenarios (and the VAT consequence)

Live hogs/cattle/chickens only (wholesale to abattoirs/traders):
- Status: VAT-exempt even beyond ₱3M → No VAT registration required for those sales.
Live hogs + house-branded hams/sausages:
- Mixed seller. Cross ₱3M total → VAT registration required.
- Invoices: Live hogs as VAT-exempt; processed meats at 12% VAT.
Fighting cocks/game birds (no food purpose):
- Taxable goods. Cross ₱3M → mandatory VAT. Below ₱3M → choose VAT or small-taxpayer route.
Meat shop buying live hogs and selling fresh, chilled, or frozen cuts (no curing/smoking/canning):
- Often still within “original state” food exemption (simple cutting/chilling). If exclusively this line, VAT-exempt regardless of volume. Add processed lines (marinated, smoked, canned) → mixed seller rules apply.
Exports of live animals/meat:
- If the product is VAT-exempt by nature locally, it remains exempt (not zero-rated) even if exported. If you export a VAT-taxable product and you are VAT-registered, that export can be zero-rated (subject to documentary rules).

Percentage tax (small-taxpayer) vs. VAT for livestock

The small-taxpayer percentage tax regime applies to non-VAT sellers of taxable goods/services not exceeding ₱3M.
Sales that are VAT-exempt by nature (like original-state food livestock) are generally not subject to percentage tax in the first place.
Once you VAT-register (because you crossed ₱3M or opted in), percentage tax no longer applies to your taxable lines; you file VAT instead. (Exempt lines stay exempt.)

(Note: Congress has, at times, adjusted the percentage-tax rate temporarily; always apply the rate in force for your taxable year.)

Compliance checklist (what to actually do)

Map your product list into VAT-exempt vs VAT-taxable.
Monitor gross sales/receipts YTD (rolling 12-month or calendar year) to see if/when ₱3M will be exceeded.
If you’ll exceed ₱3M and you have any taxable lines, update with BIR to VAT (Form 1905) and secure authority to print VAT invoices/receipts.
Adjust pricing: If you were non-VAT and become VAT, decide whether to add VAT to your price or treat prices as VAT-inclusive (mind customer contracts).
Set up input VAT allocation for mixed activities; keep VAT-qualified invoices from suppliers.
Disclose properly on invoices: mark “VAT-Exempt Sale” for original-state livestock; show 12% VAT for taxable lines.
File and pay on time: VAT returns (and any applicable withholding, income tax), keep books, and maintain invoicing compliance.

Computation quickies

Late-registered seller of taxable goods:
- You billed ₱1,120,000 without stating VAT after you should have been VAT-registered.
- BIR treats price as VAT-inclusive:
  - Output VAT = 1,120,000 ÷ 1.12 × 12% = ₱120,000
  - Net sale (Vatable base) = ₱1,000,000
- Add surcharge and interest per NIRC if assessed.
Mixed seller allocating input VAT:
- Total input VAT for the quarter: ₱300,000.
- Sales mix: ₱6,000,000 taxable, ₱4,000,000 exempt.
- Attribution: If not directly attributable, allocate by sales ratio.
  - Creditable input VAT = 300,000 × (6,000,000 / 10,000,000) = ₱180,000.
  - ₱120,000 is non-creditable (expense).

Frequent pitfalls

Assuming the ₱3M rule forces VAT on exempt livestock—it doesn’t. The nature of the goods (original-state food) controls.
Issuing VAT invoices for exempt sales (and collecting “VAT”)—this creates unlawful VAT collection and potential assessments/refunds.
Failing to segregate exempt vs taxable lines—this leads to disallowed input VAT or underdeclared output VAT.
Not updating to VAT once you add a taxable line and breach ₱3M*—expect assessments.

Bottom line

Exclusively original-state food livestock sellers remain VAT-exempt even if annual sales blow past ₱3,000,000—no VAT registration is required for those sales.
If you sell any taxable goods/services (e.g., fighting cocks, processed meats, ancillary taxable services) and your gross annual sales/receipts exceed ₱3M, VAT registration becomes mandatory.
Mixed sellers must register once they cross ₱3M, charge VAT only on taxable lines, keep exempt lines VAT-free, and allocate input VAT carefully.
Clean invoicing, timely registration updates, and robust books will save you from the classic assessments.

If you want, tell me your exact product list and last 12 months’ monthly sales (split by item), and I’ll map your VAT/exempt mix, flag if/when you cross ₱3M, and draft the registration and invoicing steps tailored to your setup.