Innovation is a clear target of the Europe 2020 growth strategy. It has been widely postulated that cooperation is especially important for innovation in the food industry because it has traditionally been regarded as a “low tech” sector. This paper analyses how different forms of cooperation affect innovation activities in the EU’s food industry. In particular, the study addresses the question of how cooperation between companies and key chain agents influences innovative activity. To do so, we analysed data at the country level drawn from the Community Innovation Survey (CIS). The aggregated data allowed us to investigate national system-level processes that must be considered the outcomes of micro-level decisions and policies. A random effect linear model is formulated and estimated to analyse the panel data obtained from five CIS waves. The model indicates that cooperation with universities positively affects innovative activity and, surprisingly, that government financial support has not been an effective instrument to foster innovation by food companies.