The increased concern about the capacity of (inter)national agricultural research to create societal impact urges research to reflect on its role in society and to adopt an innovation systems approach, enhancing multilevel stakeholder learning and negotiation for new technologies and institutional and organisational arrangements (e.g. World Bank 2012). But what does this mean for practice? This paper reflects on the joint learning process undertaken by a research consortium consisting of three African national research teams and four European teams. Its purpose was to study innovation processes in the framework of the EU-funded multipartner project JOint Learning in Innovation Systems in African Agriculture (JOLISAA). The project was implemented in 2010-13 in Benin, Kenya and South Africa, where innovation cases were inventorised, selected, screened and collaboratively assessed by multistakeholder teams. Results indicated that researchers learnt about innovation from the cases they studied and about the interaction with the stakeholders in the individual case assessments and from other collaborative assessment teams. The project duration was too short and the resource base too limited for adequate development of the concepts used, and the diverging views on what joint learning in the project meant hindered the development and implementation of a learning agenda. We conclude that integrated multistakeholder approaches that combine participatory research activities with reflective learning and capacity building for all research participants are highly desirable but not easy to implement. They require longer timespans to develop effective partnerships.