Innovation and knowledge exchange are receiving increased attention among policy makers as a means to address sustainable economic development challenges (European Commission, 2011). However, a range of factors such as inappropriate structures and institutional or capabilities barriers may negatively influence the spread or direction of processes of innovation and knowledge exchange (Klein-Woolthuis et al., 2005). These problems are often referred to as systemic weaknesses or failures, and highlight the need to focus on the innovation system (IS) as a whole (Smiths and Kuhlmann, 2004; Raven et al., 2010). The purpose of the paper, using a comprehensive innovation systems failure framework, is to assess and he performance of agrifood innovation systems of Scotland and the Netherlands, through analysis of the key innovation actors (organisations, networks or influential individuals), and their key functions (research provider, intermediary etc), and those mechanisms that either facilitate or hinder the operation of the IS (known as inducing and blocking mechanisms, respectively). This framework was drawn up based on literature research and a series of semi-structured interviews and/or workshops with experts involved in the agrifood innovation systems in the two countries. The findings confirm the appropriateness of considering actors, functions, inducing or blocking mechanisms and governance instruments as analytical tools to evaluate the performance of agrifood innovation systems. In both countries, blocking mechanisms in terms of actors’ interactions and competencies as well as market and incentive structure were revealed. The proposed mix of governance mechanisms in each country offers actors a better chance to influence the direction and speed of innovation in agrifood systems.