Agricultural Exports from Kenya: Mombasa Port and JKIA Guide

Moving fresh produce from Kenya takes coordination between growers, packhouses, inspectors, clearing agents and carriers. This guide explains the main sea-freight checkpoints at Mombasa Port and the air-cargo process at JKIA, from preparing documents to confirming departure. Use it to plan responsibilities and handovers with your supplier and importer. Requirements vary by commodity, destination and current official notices; confirm the applicable approvals before dispatch. For seasonal availability, see the Kenya harvest calendar.

Use the guide to coordinate:

• Sea freight: export documentation, container stuffing, seals, Verified Gross Mass and terminal gate-in.
• Air freight: cargo acceptance, phytosanitary inspection, customs release and confirmed uplift.
• Buyer requirements: traceability, destination protocols, cold-chain handling and shipment evidence.

Flowers, food produce, coffee and tea do not all share an identical permit checklist. Work with the appointed licensed clearing agent, relevant regulators and carrier.

Document rule: Maintain a Commercial Invoice and Packing List for each shipment. Establish which Certificate of Origin is required for the destination, preferential claim or buyer's contract; do not assume a preferential certificate is universal. Obtain the required Phytosanitary Certificate for regulated plant consignments and satisfy the importing country's plant-health requirements. Keep transport and customs references consistent across the file.

Section 1: Mombasa Port Export Procedure for Agricultural Goods

1. Establish online access and appoint the declarant

For the Mombasa port export procedure, register the business and nominated users through KenTrade's registration service, complete the applicable registration and training process, and obtain access to the Trade Facilitation Platform, Kenya's National Electronic Single Window. The KenTrade single window system supports agency approvals; confirm the relevant AFA and KEPHIS registrations separately. KenTrade registration procedure

Appoint a licensed clearing agent with authorized KRA iCMS access. KenTrade coordinates agency permits and related trade information; it does not replace the customs export declaration in iCMS. Have the agent verify the exporter's PIN, classification, declaration procedure and invoice requirements before submission. KRA iCMS export notice

Documents at setup: Business registration, KRA PIN, agent authorization and applicable exporter licences. For the consignment, prepare the Commercial Invoice, Packing List and a register of required origin and phytosanitary documents.

2. Apply the ACD requirement to the correct trade direction

Kenya's ACD requirement covers containerised cargo destined for Kenyan ports. It is not a general requirement for Kenya-origin exports leaving Mombasa. For applicable inbound cargo, obtain the validated ACD before loading at the overseas origin and endorse the reference on the Bill of Lading. KRA requests the draft Bill of Lading, Commercial Invoice, Freight Invoice and Export Declaration. KRA ACD notice

Carrier guidance describes a 15-character alphanumeric reference, often called a 15-digit code. It is not necessarily numeric. For outbound Kenyan produce, check the destination's separate advance-cargo or cargo-tracking rules and the carrier's instructions. Maersk Kenya ACD guidance

3. Align African produce sourcing with plant-health requirements

Confirm traceable growers, current export permission, buyer specifications and the destination's import conditions. For horticultural exports, verify applicable AFA farm and packhouse compliance before packing. Arrange the required consignment inspections; a facility inspection does not replace shipment-level plant-health checks.

Apply for inspection and the required KEPHIS phytosanitary certificate through its Integrated Export Import Certification System (IEICS). Coordinate the agreed inspection location, sampling access and resolution of non-conformities. Do not dispatch fruit merely because an application has been submitted. KEPHIS services, KEPHIS application procedure

For buyers importing avocado from Kenya, align the sourcing brief with current export permission, mature fruit availability and the destination protocol before committing to a loading date.

Documents at inspection: Commercial Invoice, Packing List, consignment/UCR reference where required, traceability and packhouse records, applicable AFA approvals, and the destination's import permit or phytosanitary conditions. The Phytosanitary Certificate is an output of satisfactory certification, not something already available at the first inspection request. Prepare the Certificate of Origin where required for the trade lane.

4. Book, stuff and seal the reefer

Confirm these reefer booking and cold-chain controls before loading:

• Vessel booking, equipment type, terminal receiving window and documentary cut-offs.
• Reefer fitness, carrier instructions and produce pre-cooling to the agreed commodity specification.
• Loading arrangements that protect airflow, with container and seal numbers recorded.
• Customs verification or supervision required before sealing.
• Temperature settings and written handover instructions.

Documents at loading: Invoice, Packing List, booking confirmation, required permits and certificates, customs reference or instructions, and the stuffing/seal record. Reconcile final weights and quantities before issuing shipping instructions.

5. Submit Verified Gross Mass and clear port payments

Obtain Verified Gross Mass (VGM) using an accepted SOLAS-compliant method. VGM includes the packed container's contents, packaging, securing material and container tare; it is not the produce net weight. Submit it to the carrier and KPA according to their cut-offs and pre-advice requirements. KPA's published procedure requires VGM in pre-advice before gate-in. KPA VGM procedure

Settle applicable KPA invoices through the official KPA eCitizen service and retain receipts. Settle carrier and other service-provider charges through their authorized channels; they are not automatically included in KPA payments.

Documents at this checkpoint: Signed VGM declaration and supporting weighing record, container/seal details, booking reference, port invoice and payment receipt. Keep the Invoice, Packing List and permit file available for reconciliation.

6. Enter the port and complete directed controls

Confirm truck and personnel access, the nominated gate, export pre-advice and terminal acceptance before trucking. At gate-in, reconcile container identity, seal, booking and cargo documentation. Keep the reefer powered in accordance with the transport and terminal plan.

Follow Customs' assigned scanning, examination or direct-release instructions. Do not describe X-ray scanning as universal: controls depend on Customs routing and other applicable security requirements. Resolve any seal, weight or documentation discrepancy through the authorized parties before onward movement. KPA security controls, KRA verification and release

Documents for verification: Customs export entry and supporting Commercial Invoice, Packing List, Phytosanitary Certificate, applicable Certificate of Origin and commodity permits; booking, VGM, container/seal and payment references as requested. A final shipped-on-board Bill of Lading normally follows loading rather than preceding every gate check.

7. Confirm customs release, loading and departure

Track the customs release and carrier loading acceptance separately. Gate-in or customs release alone is not proof that the vessel carried the cargo. Obtain loading/departure confirmation, check the final Bill of Lading and arrange the customs export confirmation or Certificate of Export through the agent after actual exit is confirmed. KRA export process

Close-out file: Final Invoice and Packing List; required Phytosanitary Certificate and Certificate of Origin; relevant permits; released customs entry; Bill of Lading; departure evidence; and customs export confirmation. Retain cold-chain and seal records.

Section 2: JKIA Air Freight Logistics for Fresh Produce

1. Build the plan backwards from the flight cut-off

For JKIA air freight logistics, confirm the following before harvest or dispatch:

• Flight capacity and the nominated airline's cargo handler.
• Cargo acceptance location, security screening and cold-storage arrangements.
• Separate cut-offs for documentation, inspections, cargo acceptance and flight build-up.

Herbs, flowers and fresh vegetables require product-specific temperatures and handling; one generic setting is unsuitable.

Documents before dispatch: Commercial Invoice, Packing List, booking/Air Waybill reference, buyer specifications, destination import conditions and applicable permits. Establish the Certificate of Origin requirement and phytosanitary certification route early.

2. Lodge the customs export entry

Have the appointed agent submit the export declaration through KRA iCMS, using the correct exporter, commodity classification, quantities and transport details. Track processing and resolve document queries before the cargo cut-off. Complete the required agency approvals through KenTrade and the relevant regulator's system.

Documents for lodging: Invoice, Packing List, Air Waybill/booking information, required permits and available certificates, including the required Certificate of Origin and Phytosanitary Certificate at the stage directed by Customs. An entry number alone does not authorize loading. KRA customs process

3. Confirm and pay applicable airline, handling and concession charges

Request an itemised invoice from the airline, handling agent or relevant authority. Verify who levies each charge, its current basis and the accepted payment channel. Do not publish a universal current “airline concession fee”: the reviewed current primary sources do not establish one standard charge for all JKIA fresh-produce exports. Obtain the live tariff or invoice before quoting it.

Documents at payment: Booking/Air Waybill reference, supplier invoice for the service, payment authorization and official receipts. Keep these distinct from the Commercial Invoice for the produce.

4. Present cargo at the nominated customs shed or handler facility

Route the consignment to the location specified by the agent and airline; do not assume there is one universal shed for all JKIA exports. Complete access, receiving, weighing and security screening requirements. Match packages and labels to the Packing List and record cargo condition and cold-chain handover.

Documents at receiving: Packing List, Invoice, Air Waybill/booking reference, customs entry reference and required approvals. Have the Phytosanitary Certificate and relevant Certificate of Origin available in the accepted form and by the required documentary cut-off.

5. Complete phytosanitary and physical verification

Coordinate KEPHIS inspection at the approved inspection point and obtain the required phytosanitary certification. KEPHIS checks conformity with destination plant-health conditions; Customs verifies the declaration and cargo as directed. Security screening is a separate control. Schedule activities together where permitted to limit exposure of highly perishable cargo. KEPHIS inspection requirements

If packages are opened, record quantities, repacking, revised weights and any seal changes. Restore appropriate storage promptly. Complete any additional AFA, Port Health or commodity-specific checks required for the particular consignment.

Documents at verification: Invoice, Packing List, customs entry, Air Waybill reference, applicable licences and permits, traceability records, Phytosanitary Certificate or pending certification record as appropriate, and the required Certificate of Origin. Resolve inconsistencies before requesting release.

6. Obtain the passed entry and final release

Ask the agent to confirm the current passed-entry status and customs release authorization in iCMS, including any endorsements required by the cargo facility. “Pass Entry” should describe an actual passed customs entry, not be presented as a separate universal certificate issued after departure.

Obtain airline/handler acceptance once customs, agency and security requirements are satisfied. Release permits movement or loading under the applicable procedure; it does not prove the flight departed. KRA passed-entry and release explanation

Documents at release: Passed/released customs entry, applicable agency clearances, Phytosanitary Certificate, Invoice, Packing List and Air Waybill details. Include the required Certificate of Origin in the shipment document pack.

7. Confirm uplift and obtain export evidence

Verify actual flight uplift and departure with the airline or handler. Have the clearing agent complete export confirmation and retrieve the Certificate of Export and its reference/number, as issued by Customs. This follows confirmation of export; it should not be promised as a pre-flight gate pass. KRA Certificate of Export sequence

Close-out file: Final Invoice, Packing List, Air Waybill, required Certificate of Origin, Phytosanitary Certificate, relevant permits, customs release, uplift/departure confirmation and Certificate of Export reference. Notify the destination importer and flag any short-shipment immediately.

Dosano coordination standard

Maintain one shipment reference and one accountable coordinator. Record the current document status, actual carrier cut-offs, inspection bookings and outstanding holds. Confirm the official position before dispatch when a permit, fee, system status or seasonal restriction is unclear. Do not substitute a payment receipt, gate acceptance or booking confirmation for regulatory release or proof of export.

Plan sourcing and export logistics together

Use the Kenya harvest calendar to connect seasonal availability with your sourcing brief. Follow the supplier journey to align commercial terms, counterparty checks, inspection preparation and shipment handovers. These planning resources support agricultural exports from Kenya without replacing current regulatory approvals or confirmed carrier capacity.

Discuss your shipment: Contact Dosano Logistics Kenya with your product, grade, volume, origin and destination.