In the National Innovation System (NIS), knowledge is produced and accumulated through interactive innovation processes that are embedded in a national context, which in turn may help determine innovation. This paper investigates how product and process innovations in the European food and drink industry are affected by: (i) NIS structure; (ii) NIS output in terms of scientific publications and the supply of graduates; (iii) NIS cohesion and coordination; (iv) NIS scientific impact and specialisation. The main source of data on innovation by firms is the EU‐EFIGE/Bruegel‐UniCredit dataset. This is supplemented by information from the International Handbook of Universities, Eurostat and a bibliometric analysis of academic research output. Our results suggest that large research institutions in the public sector may well be detrimental to interaction between university and industry and to process innovation. The indicators used for public research assessment are not necessarily the most appropriate proxies of local knowledge spillovers.