Kenya’s horticultural sector, cut flowers, fresh vegetables, fruit, and nuts, is one of the country’s largest foreign exchange earners, and exporting any of it commercially requires clearing two distinct regulatory gateways rather than one. A grower or exporter needs an export licence from the Horticultural Crops Directorate to operate as a horticultural exporter at all, and separately needs a phytosanitary certificate from the Kenya Plant Health Inspectorate Service for every individual consignment that leaves the country. Missing either step, not just both, can result in produce being held, rejected at the border, or destroyed.

The Two Regulators and What Each One Controls

The Horticultural Crops Directorate, commonly known as HCD, operates under the Agriculture and Food Authority and was established pursuant to the Crops Act 2013. HCD’s role is to regulate who may commercially export horticultural produce from Kenya in the first place: any entity exporting fresh fruits, vegetables, or flowers on a commercial basis must hold an HCD export licence, which is renewed annually.

The Kenya Plant Health Inspectorate Service, commonly known as KEPHIS, was established in 1996 and operates under the Plant Protection Act, Chapter 324, and the Agricultural Produce (Export) Act, Chapter 319. KEPHIS’s role is different in kind from HCD’s: rather than licensing the exporter as a business, KEPHIS certifies that each individual consignment is free from regulated pests and diseases before it is permitted to leave the country, in line with the International Plant Protection Convention and the World Trade Organisation’s Sanitary and Phytosanitary Agreement. A business can hold a valid HCD licence and still have an individual shipment rejected by KEPHIS if that specific consignment fails phytosanitary inspection.

Obtaining an HCD Export Licence

To register as a horticultural exporter with HCD, an applicant generally needs to provide a certified copy of the certificate of business registration or incorporation, a certified copy of the company’s KRA PIN, a certified copy of the memorandum and articles of association where the applicant is a company, identification documents for all directors, documentary evidence of an overseas buyer relationship such as a purchase order or supply agreement, a phytosanitary statement from KEPHIS covering the relevant calendar year, and evidence from a Good Agricultural Practices farm and packhouse inspection. Applicants are also required to demonstrate access to appropriate packhouse and cold chain infrastructure, either through their own facilities or through arrangements with a third-party logistics and storage provider, and typically need a county government business permit from the relevant sub-county office before the HCD application can proceed.

Once the application documentation is complete, applicants present themselves for vetting at HCD headquarters, where officials review the file against a published checklist before the licence is granted.

Registering for Phytosanitary Certification

Separately from the HCD licensing process, every exporter must register on the KEPHIS Integrated Export Import Certification System, accessible online, providing the company or cooperative’s name, KRA PIN, registered business address, and the crop types intended for export. Each production site supplying the consignment must be individually registered with KEPHIS, recording field location, crop type, and area under production, and the packhouse used for sorting and packing must separately pass a KEPHIS hygiene and traceability inspection before it can be used to prepare export consignments.

For each shipment, the exporter applies for pre-export inspection, generally required at least 48 hours before the planned export date. KEPHIS inspectors examine the consignment for pest and disease status, verify labelling accuracy, and confirm produce identity, before issuing the phytosanitary certificate that must accompany the shipment to the border. KEPHIS maintains inspection points at Jomo Kenyatta International Airport cargo terminal for air freight, at Mombasa Port for sea freight, and at a number of regional offices for produce moving by other routes.

The Plant Protection Regulations 2021

The Plant Protection (Import and Export) Regulations 2021 provide more detailed procedural requirements sitting beneath the parent Plant Protection Act, including the certification standards for quarantine facilities, treatment requirements for materials such as wood packaging used in export consignments, and the documentation an applicant must submit when seeking authorisation to operate as an inspection body or quarantine facility. These regulations also confirm that any phytosanitary authorisation granted is additional to, and does not substitute for, any other licence or permit required under separate legislation, which is a useful reminder that HCD and KEPHIS requirements operate cumulatively rather than as alternatives to one another.

Genetically Modified Material and Biological Control Agents

Where export or import activity involves genetically modified plant material, separate clearance from the National Biosafety Authority is required before KEPHIS will issue a permit for the material, and the National Biosafety Authority’s board draws representation from KEPHIS, the Ministry of Agriculture, and several research and academic institutions. Similarly, the importation of biological control agents is vetted by the Kenya Standing Technical Committee for Imports and Exports, with KEPHIS conducting the underlying facility inspections to confirm import conditions are properly observed. These additional layers are most relevant to exporters working with novel crop varieties or biological pest control inputs rather than conventional fresh produce, but they are worth flagging early where they apply, since the additional clearance can add meaningfully to project timelines.

Buyer-Driven Certification Standards

Beyond the statutory HCD and KEPHIS requirements, most international buyers, particularly in the European Union and United Kingdom, require additional private certification before they will accept Kenyan produce into their supply chains, most commonly GLOBALG.A.P or the locally recognised KenyaGAP standard covering good agricultural practice on the farm. These are not government licensing requirements in the strict legal sense, but for practical purposes they function as a parallel compliance gateway, since failing to meet them closes off the export markets that justify the cost of HCD and KEPHIS compliance in the first place. Exporters structuring a new horticultural venture should plan for buyer certification requirements alongside the statutory licensing process rather than treating them as a separate, later-stage concern.

Packhouse Registration and Traceability

A registered packhouse is not a formality layered on top of the licensing process; it is itself a distinct compliance requirement that KEPHIS inspects and certifies before produce passing through it can be exported. The packhouse inspection covers hygiene standards, pest exclusion measures, and the traceability systems in place to link a given consignment back to the specific farm and field where it was grown. This traceability link matters more than it might first appear: where a pest or disease issue is identified in an export consignment, KEPHIS and destination-country authorities trace the problem back through the packhouse records to the originating farm, which can result in that farm being suspended from the export supply chain pending corrective action, independent of whether the exporting company’s HCD licence itself remains valid. Exporters working through aggregators or contract farming arrangements with multiple smallholder suppliers should ensure that farm-level registration and traceability records are properly maintained across the entire supply base, not only at the level of the exporting company itself, since a gap at any point in that chain can disrupt the whole consignment.

Consequences of Non-Compliance

Produce that fails KEPHIS phytosanitary inspection is either destroyed or prohibited from leaving the country, representing a direct and often substantial financial loss on the affected consignment. Beyond the immediate loss, persistent non-compliance can affect an exporter’s standing with both regulators and with destination-country authorities, who maintain their own monitoring systems for non-compliant consignments originating from Kenya. Given the EU’s heightened documentary and physical inspection regime for certain Kenyan produce categories, exporters operating in those categories should treat compliance as an ongoing operational discipline rather than a one-time licensing exercise completed at the start of the business.

How We Can Help

Clay & Associates Advocates advises horticultural exporters, agribusiness investors, and cooperatives on HCD licensing, KEPHIS registration, and the broader regulatory framework governing agricultural exports from Kenya. If you are establishing a horticultural export business or need advice on a compliance issue affecting your export licence or consignment certification, our regulatory and compliance team can guide the process, and our experience advising manufacturers and other regulated exporters extends naturally into the documentation and compliance discipline that horticultural export businesses require.

For official guidance, see the Kenya Plant Health Inspectorate Service’s phytosanitary services page, and for the governing legislation, the Agriculture and Food Authority’s Horticultural Crops Directorate page for current licensing requirements.