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A bakery needs a sanitary permit from the city or municipal health office, and every employee needs a health certificate. If you make or repack packaged bread for other stores, FDA adds a License to Operate and product registration. What owners miss most: health certificates are renewed at least once a year, so every baker, cashier and new hire needs a current one.[1,2,4]
Selling over your own counter vs supplying stores
FDA requires a License to Operate before you manufacture, repack, distribute or sell processed food in a covered establishment. FDA's checklist gives 20 working days. Each prepackaged product also needs a Certificate of Product Registration. FDA Advisory 2025-0032 says fees for applications filed from 12 January 2025 follow the newer fee order, AO 2024-0016, so ask FDA for your amount.[4,5]
FDA's food rules exclude restaurants but do not name bakeries. A bakeshop selling only from its own counter is not expressly addressed. If you will supply sealed bread to sari-sari stores, ask FDA first.
Water: the requirement that trips up bakeries
A food establishment's water supply must be adequate and potable.[1]
Some LGUs ask for more. Morong, Rizal, for example, has bakeries, eateries and food stands submit monthly bacteriological water tests from a DOH-accredited lab for the sanitary permit.[3]
Ask your health office if your town does the same, and find an accredited lab near you before opening week.
What repeats every year
Health certificates are renewed at least yearly, or more often if a local ordinance says so.[1]
Bring new hires to the health office before they handle dough. Read more in the health certificate guide.
Before your first batch
- List every person who will handle food, including part-time helpers.
- Book health certificate exams for all of them.
- Find a DOH-accredited water lab and ask about test schedules.
- Ask the health office if your LGU requires monthly water tests.
- Decide if you will sell only at your counter or also supply other stores.
- If supplying stores, list each packaged product for FDA registration.
- Keep a folder for permits, lab results and health certificates.
Questions people ask
- Does a small bakeshop need an FDA license?
- FDA licensing covers businesses that manufacture, repack or distribute processed food. FDA's rules do not say if a bakeshop selling only over its own counter is covered. Ask FDA if you plan to supply other stores.
- How long does FDA take?
- FDA's checklist gives 20 working days for a License to Operate, and the FDA charter lists 20 working days for an initial product registration.
- Does every employee need a health certificate?
- Yes. PD 856 requires a health certificate from the local health authority for every employee of a food establishment.
- How much is the sanitary permit for a bakery?
- There is no national amount. It is set by your city or municipal ordinance.
Sources
Checked 13 November 2026. We link the agency's own page for every requirement. Rules change; confirm with the office before you pay.
- Implementing Rules and Regulations of Chapter III, Food Establishments, of P.D. No. 856 · Department of Health (text via Supreme Court E-Library) · 29 December 1995
- Presidential Decree No. 856 (Code on Sanitation of the Philippines) · Lawphil (text of PD 856) · 23 December 1975
- Requirements for Application of Sanitary Permit · Municipality of Morong, Rizal
- Administrative Order No. 2014-0029: Rules and Regulations on the Licensing of Food Establishments and Registration of Processed Food, and Other Food Products · Department of Health / FDA (text via FAO FAOLEX) · 8 September 2014
- FDA Advisory No.2025-0032 || Effectivity of Administrative Order No. 2024-0016 · Food and Drug Administration Philippines · January 2025
The extra permits, in one table
| Permit or registration | Agency | When it applies | Fee |
|---|---|---|---|
| Sanitary permit for a bakery (IRR Sec. 5(b)1)[1] | City/municipal health office (LGU) | always | set by city/municipal ordinance (IRR Sec. 3(a)3); no national amount |
| Health certificate for every food handler/employee[2] | City/municipal health office (LGU) | always | set by the city or town |
| Annual renewal of employee health certificates[1] | City/municipal health office (LGU) | always | Not published |
| Potable[1] | City/municipal health office (LGU) | always | Not published |
| Monthly bacteriological water test from a DOH-accredited lab for the sanitary permit[3] | LGU health office (example: Morong, Rizal) | where the LGU requires it (Morong lists bakeries, eateries, carinderias, food stands) | lab fee (set by the lab) |
| FDA License to Operate[4] | FDA (DOH) | if it manufactures/repacks processed food for distribution or wholesale | assessed by FDA under AO 2024-0016 (see the FDA fee row) |
| Certificate of Product Registration[4] | FDA (DOH) | if selling prepackaged products | assessed by FDA under AO 2024-0016 (see the FDA fee row) |
| FDA fees for applications filed from 12 January 2025…[5] | FDA | if it manufactures/repacks processed food for distribution or wholesale | assessed by FDA under AO 2024-0016 |