Kenya and Uganda’s newly-signed Mutual Recognition Agreement (MRA) on agricultural produce is a diplomatic document with potentially wider ramifications on regional trade and food security. Signed in Lusaka on December 4, 2025, on the sidelines of the 46th COMESA Council of Ministers meeting, it commits the two East African neighbours to recognise each other’s inspection, testing and certification of staple foods. In a region where non-tariff barriers, not tariffs, now do most of the work in blocking trade, that formal shift from suspicion to structured trust is significant.
And the timing matters because across Eastern and Southern Africa, droughts, currency weakness, and conflict are pushing up food prices, even as governments promise that the Africa Continental Free Trade Area (AfCFTA) will open regional markets.
Non-tariff barriers
Up to 70 percent of reported non-tariff barriers in the COMESA region stem from technical regulations and sanitary and phytosanitary (SPS) measures. The Kenya-Uganda MRA is one of the first attempts to address this problem at its source, by aligning how countries assess whether food is safe and meets the agreed standards.
COMESA reckons that the agreement is a key outcome of the ‘Enhancing Regional Agricultural Commodity Trade in COMESA’ project, backed by the agriculture development agency, AGRA and the UK’s Foreign, Commonwealth and Development Office (FCDO). It focuses on maize, groundnuts, soybeans, rice, beans and sorghum – the six heavily traded staples in the region.
Kenya’s Cabinet Secretary for Investments, Trade and Industry, Lee Kinyanjui, and Uganda’s Minister of Trade, Industry and Cooperatives, Francis Mwebesa, signed the pact in Lusaka with the COMESA Secretary General as the witness.
In practical terms, a mutual recognition agreement on conformity assessment means that, once the deal is fully implemented, test results and certificates issued by recognised laboratories and authorities in Kampala will be accepted by officials in Nairobi, and vice versa.
Instead of re-sampling a consignment of maize at the border and sending it for new tests, customs and SPS officers will rely on existing certificates, as long as they were issued under agreed standard operating procedures and within trusted systems.
This goes to a core friction that has, for years, slowed down regional food trade. Even where countries already share regional standards, they often do not trust each other’s enforcement. For example, maize imported into Kenya from East African Community partners must comply with the East Africa Standard EAS 2:2013, which sets limits on moisture, aflatoxin and grain quality. Yet consignments are still subjected to repeated sampling and testing on both sides of the border, raising costs and causing delays, particularly for small traders.
Research by COMESA and partners has recently shown how costly these frictions can be. One policy brief cites work in the East African Community, which found that non-tariff barriers account for about 35 percent of the total cost of moving maize across borders.
Eliminating those barriers could generate social welfare gains estimated at U$2.3 billion in Kenya, US$0.8 billion in Uganda and US$1.8 billion in Tanzania in maize and beef value chains alone.
A separate COMESA-linked analysis notes that SPS and technical measures make up the majority of reported non-tariff barriers in the bloc.
The political fallout from past food safety disputes helps explain why the new agreement is significant. In 2021, Kenya imposed a sudden ban on maize imports from Tanzania and Uganda, citing high levels of aflatoxin contamination. The East African Law Society branded the move a violation of EAC protocols and described it as yet another non-tariff barrier undermining regional integration.
Long queues of trucks formed at border posts, and traders complained of lost income and wasted stocks. While the new MRA does not stop either government from acting in a crisis, it creates a shared framework that should make unilateral bans harder to justify if trusted systems are in place.
The Lusaka signing also crowns a long and uneven technical journey. COMESA’s first attempt at a mutual recognition framework for aflatoxin-safe maize between 2015 and 2017 built common sampling protocols, laboratory proficiency testing schemes and grading systems, but collapsed before any agreements were signed, largely when funding ended.
In 2021, COMESA, AGRA and the UK’s FCDO relaunched the effort on a broader footing, covering six countries (Kenya, Uganda, Malawi, Rwanda, Zambia and Zimbabwe) and six commodities. Under that project, experts developed and validated core ‘pillars’ for mutual recognition to include harmonised sampling and inspection protocols, agreed test methods, a regional testing scheme for laboratories, and common grading criteria for grains.
In effect, this work aimed to prove that labs in Nairobi and Kampala could generate comparable results, and that inspectors were working to the same rules at silos, warehouses and border posts.
Even with those technical foundations, politics proved a drag. COMESA’s own policy brief notes that getting MRAs cleared and signed has taken more than four years, slowed by the political nature of legal vetting and the failure to fully fund key governance bodies such as the project steering and technical committees. The Kenya-Uganda deal, and an earlier MRA between Malawi and Zambia signed in Lusaka, suggest those bottlenecks are now easing, but they also show why implementation cannot be taken for granted.
The new agreement is, therefore, best read as a bridge between technical alignment and real-world trade. If it works as intended, a trader moving a truck of maize or beans from Uganda into Kenya will face fewer duplicative tests and shorter waiting times at the border.
The direct savings are fees for laboratory tests and inspections. The indirect gains are lower spoilage, fewer informal payments and more predictable delivery schedules. For small and medium-sized enterprises, which COMESA identifies as central to regional economy, those margins can decide whether cross-border trade is viable.
There are, however, reasons for caution. A recent study on SPS barriers under the Africa Continental Free Trade Area (AfCFTA) highlights persistent weaknesses in African non-tariff barriers, including inconsistent legal frameworks, under-resourced regulators and limited infrastructure such as accredited labs and cold storage.
These structural gaps mean that, even with an MRA, enforcement at busy border posts like Busia and Malaba could remain uneven. Some officials may continue to re-test consignments out of habit or fear of blame if something goes wrong, while traders may struggle to secure certificates from recognised labs in rural areas.
Food safety advocates also worry that mutual recognition can be misused to lower standards if governments recognise each other’s systems before they are fully equivalent. That means the credibility of the Kenya-Uganda arrangement will depend on how rigorously these safeguards are applied, and how transparent governments are about lab performance and incident reporting.
Meanwhile, the digital side of the agenda remains unfinished. One of the original project objectives was to design and pilot an electronic MRA system, embedded in COMESA’s planned Digital Free Trade Area and regional single window. That would allow certificates and test results to move electronically, reducing the scope for forgery and easing verification.
Yet project documents note that work on this ‘e-MRA’ has lagged, partly because the broader COMESA digital trade infrastructure is still under development and partly because partners agreed to get the legal agreements in place first.
Ultimately, the Kenya-Uganda signals to other COMESA States that political leaders are willing to sign what technocrats have spent years preparing. If more pairs of countries follow, the bloc could gradually stitch together a web of mutual recognition arrangements that, in effect, create a zone of trusted standards for key staples across Eastern and Southern Africa. And in the broader AfCFTA context, this is one of the more concrete examples of how regional economic communities can advance continental goals.
But even with the agreement signing milestone, parliamentarians and line ministries in Nairobi and Kampala still need to domesticate the MRA into national law and practice. Border agencies must train staff, update manuals and align internal incentives so that officers actually rely on recognised certificates. If, over the next two to three seasons, traders report fewer disputes over test results, shorter clearance times and lower costs, the Kenya-Uganda MRA will stand as proof that technical cooperation can move the dial on food security.