Innovation is receiving increased attention among policymakers as a means of addressing sustainable economic development challenges. However, a range of factors such as inappropriate physical and knowledge infrastructures, incoherence of institutional frameworks, or lack of specific capabilities may have a negative impact on the functioning of the agricultural innovation system. The purpose of this paper is to apply a comprehensive innovation systems analytical framework, reconciling analyses of systemic structures, functions, failures and merits of innovation systems to assess and compare the performance of the agricultural innovation systems of Scotland and the Netherlands. To achieve this an analytical framework was drawn up based on the available literature, and through a process that included document analysis and a series of semi-structured interviews and workshops with experts in the two countries the agrifood sectors were empirically assessed. In both countries, systemic failures in terms of actors’ interactions and competencies as well as market and incentive structures were revealed. However, differences emerge between the two countries that appear to relate more to social and cultural (soft institutions) differences rather than the formal legal and regulatory frameworks (hard institutions)