Digitalization of Phytosanitary Certificates for Exporting Products

International agrifood trade moves millions of tons of plant products between countries with different phytosanitary requirements every year. Each shipment requires a phytosanitary certificate proving compliance with those requirements. Any documentary error can result in border rejections, spoilage of perishable goods, and direct economic losses for the exporter.

The digitalization of this process is already underway. The ePhyto system, promoted by the International Plant Protection Convention (IPPC), makes it possible to transmit electronic certificates between authorities in different countries. Technologies such as blockchain add an additional layer of traceability and documentary integrity that strengthens trust across the entire export chain.

A phytosanitary certificate is an official document issued by the phytosanitary authority of the exporting country certifying that a shipment of plants or plant products complies with the requirements of the destination country and is free of regulated pests. International Standard for Phytosanitary Measures No. 12 (ISPM 12), published by the International Plant Protection Convention (IPPC), establishes the framework governing its content, format, and conditions of issuance.

The phytosanitary certificate performs the following functions in international agrifood trade:

Risk control. It demonstrates that the shipment has been inspected to prevent the introduction of plant pests and diseases into the importing country.

Regulatory compliance. It serves as proof that the exporter has met the plant health requirements of the destination market.

Contractual and logistical support. Its presentation is often a condition for the release of the goods through customs and for payment execution through documentary credits.

International harmonization. By following standardized formats set by the IPPC, it facilitates interoperability and trust among authorities in different countries.

According to the FAO, preventing the arrival of even a single quarantine pest can save a country billions in agricultural damage and eradication costs.

Who issues phytosanitary certificates in Spain and in the rest of the world?

In Spain, the Ministry of Agriculture, Fisheries and Food (MAPA) acts as the National Plant Protection Organization and is the only competent authority authorized to issue export phytosanitary certificates. The process is carried out through the Health Information and Phytosanitary Surveillance System (SISVF), regulated by Royal Decree 387/2021.

The exporter first consults MAPA’s phytosanitary requirements database to learn the requirements of the destination country. It then submits the application to the Plant Health Inspection Services at the point of departure, which manage issuance through the CEXVEG application. The system relies on the operator’s declarations of responsibility, technical documentation, and attestations from regional plant health services. In the European Union, each Member State maintains its own NPPO (National Plant Protection Organization), the international term for national plant protection organizations, but the European Commission has centralized document exchange through TRACES-NT, which connects to the ePhyto Hub. Outside Europe, the same pattern is repeated with USDA-APHIS in the United States, DAFF in Australia, or SENASICA in Mexico. The constant is that the issuing authority is always public, with varying degrees of territorial decentralization and strong support from interoperable information systems.

Types of phytosanitary certificates and requirements by market

ISPM 12 distinguishes between two main types of phytosanitary certificates. The export certificate is issued by the NPPO of the country where the plant products were grown or processed and certifies compliance with the importer’s requirements. The reexport certificate is issued by the NPPO of an intermediate country when the goods are reshipped to a third destination without having been transformed.

The applicable requirements vary depending on the destination country, plant species, and product type. They may include visual inspection, mandatory treatments such as fumigation or cold treatment, origin from pest-free areas, laboratory testing, and specific packaging conditions. In Spain, MAPA provides protocols negotiated product by product and country by country that operators must consult before planning any export, as reported by IFEMA.

TRACES-NT links the phytosanitary certificate with other control documents such as the CHED-PP, thereby integrating plant health and food safety in a single workflow. This integration makes it easier for companies to manage in a coordinated way all documentary certification with legal validity accompanying their shipments.

The ePhyto revolution: from paper to the electronic phytosanitary certificate

ePhyto is the electronic version of the phytosanitary certificate, issued in XML format and transmitted between phytosanitary authorities through the IPPC’s global Hub. It has full legal equivalence with the paper certificate and allows NPPOs to exchange, validate, and approve certificates securely, directly, and without relying on the physical shipment of documents.

The ePhyto system is structured around three complementary elements. The global Hub acts as a secure messaging bus between NPPOs, using encrypted transport protocols that guarantee integrity and confidentiality. The GeNS (Generic ePhyto National System) is a generic system that the IPPC offers to countries without their own infrastructure to produce, send, and receive ePhytos via the web. Countries with developed national systems, such as TRACES-NT in the European Union, connect to the Hub to exchange electronic certificates with the rest of the members.

The European Union has made acceptance of electronic phytosanitary certificates provided through TRACES-NT mandatory, in accordance with Regulation (EU) 2016/2031. According to the Global Alliance for Trade Facilitation, the transition to ePhyto can save around 1.9 million hours and more than 6 million dollars annually in certain trade corridors.

Direct NPPO-to-NPPO transmission reduces fraudulent certificates, data reentry errors, and verification times at the border. It also facilitates integration with other electronic trade systems, customs, and single-window platforms.

The digitalization of phytosanitary certificates reduces documentary friction throughout the export chain. Companies operating with ePhyto and integrated traceability systems manage their shipments with fewer border delays, fewer rejections due to formal errors, and greater control over compliance with the requirements of each market.

The use of systems such as CEXVEG, TRACES-NT, and ePhyto makes it possible to manage applications, issuance, and documentary transmissions remotely, eliminating in-person procedures and international courier costs. Advance receipt of ePhytos by the importing country shortens waiting times at the border, a determining factor for perishable goods such as fruits and vegetables.

The automatic integration of destination-country-specific requirements into the workflow prevents inconsistencies between commercial documentation and the phytosanitary certificate, as reflected in EPPO certification guidelines.

In markets with growing requirements for traceability and sustainability, the ability to provide digital data on origin, agronomic practices, and chain of custody together with the phytosanitary certificate becomes a differentiating factor compared to competitors operating with manual processes.

Traditional agrifood traceability systems, based on centralized databases and barcodes, present limitations in data integrity, interoperability among participants, and trust in environments with multiple stakeholders. The combination of technologies such as RFID with blockchain and cryptographic algorithms provides substantial improvements in transparency, integrity, and resistance to record tampering.

Blockchain technology provides a distributed ledger in which each participant has a synchronized copy of the records, reducing information asymmetries. Immutability guarantees that recorded data is verifiable without the possibility of inadvertent alteration. Timestamps and digital signatures make it possible to reconstruct the full history of a product, and smart contracts allow automation of business rules linked to events in the chain.

These properties are useful for documenting that a shipment has complied at all times with phytosanitary and cold chain conditions, and for proving it to importers and authorities. The trend points toward hybrid systems in which operational data is stored in centralized databases and the hashes of critical events are anchored in a legally valid blockchain infrastructure to ensure integrity.

Do you export agricultural products and want to strengthen the traceability and certification of your shipments? Discover how ISBE, Spain’s first blockchain infrastructure with legal validity, can help you enable your phytosanitary certification operations with a digital product passport that is verifiable throughout Europe.

What is the validity period of a phytosanitary certificate from the time it is issued?

There is no universal time period. Validity depends on the combination of decisions made by the exporting NPPO and the requirements of the importing country, and it is usually between 10 and 30 days from the date of inspection or issuance until the shipment departs. In Spain, the effective deadlines are determined by the protocols MAPA maintains with each destination country.

Is a phytosanitary certificate mandatory for processed or cooked agricultural products?

It is not mandatory in all cases. If processing eliminates the product’s capacity to carry pests, as is the case with flours, canned goods, or cooked products, a phytosanitary certificate is generally not required. However, minimally processed products, such as nuts or dried goods, may still require it depending on the importing country’s regulations. It is advisable to consult the specific requirements of each destination.

What legally happens if the goods arrive at their destination and the original certificate has been lost?

In the paper-based model, the exporting NPPO may issue a duplicate or replacement certificate referencing the original. During that process, the goods may be held in customs storage, with the associated storage costs and product losses. With ePhyto, the impact is smaller because transmission is direct between NPPOs and verification does not depend on the physical document.

Can a phytosanitary certificate be modified or corrected once it has been issued?

It cannot be altered freely. The NPPO may issue a replacement certificate to correct formal errors such as quantities or typographical data, always referencing the original. Substantive changes in species, origin, or treatments require a new inspection and a new certificate. In ePhyto environments, a new electronic message is issued that replaces the previous one with the corresponding traceability.

The export certificate is issued by the NPPO of the country where the plant products were grown or processed. The reexport certificate is issued by the NPPO of an intermediate country that is not the country of origin, when the goods are reshipped to a third destination without having been transformed. This second certificate must be accompanied by the original or by a certified copy from the country of production.