Pests and diseases are key production constraints for Ugandan small-scale farmers. In 2010, the Ugandan Government, as part of its agricultural development strategy, adopted plant clinics to improve plant health extension for farmers and to contribute to strengthening disease surveillance. Despite government commitment and a growing demand for this new type of farmer service, effective implementation of plant clinics turned out to be a challenge. We examine how agricultural policies and institutional setups, and their political context, influenced the implementation of plant clinics from 2010 to 2011. We argue that the political agenda surrounding the decentralization and agricultural extension reforms, initiated in 1997, substantially weakened the Ministry of Agriculture, Animal Industry and Fisheries and undermined institutional stability and the effectiveness of delivery of public extension services. Implementation of plant clinics was further affected by a new district reform and the national elections taking place during the study period. The dual purpose of the plant clinics created uncertainty about their organisational belonging. They fell through the cracks of extension and disease control. This was exacerbated by the unclear roles and authority of the Ministry vs. local governments. For plant clinics to succeed the fundamental issues of governance, resources and implementation structure need to be addressed. The Ugandan experience shows the importance of understanding not only the policy and institutional frameworks in which plant clinics operate, but also the effects of political imperatives and donors on policy implementation. This study provides a basis for institutional and policy analysis related to the implementation of plant clinics elsewhere.