According to the National Innovation System (NIS) approach, the innovative capabilities of a firm are explained by its interactions with other national agents involved in the innovation process and by formal and informal rules that regulate the system. This paper intends to verify how product and process innovation in the European food and drink industry are affected by: i) the NIS structure in terms of universities vs public research labs, faculties/department mix and size; ii) the NIS output in terms of WoS indexed publications vs the supply of graduates; iii) the NIS fragmentation and coordination and iv) the NIS scientific impact and specialisation.The source of data on firm innovation is the EU-EFIGE/Bruegel-UniCredit dataset supplemented by information from the International Handbook of Universities, Eurostat and the bibliometric analysis of academic research quality. The results obtained suggest that large size of public research institutions are detrimental to interactions between university and industry and the indicators used for public research assessment are not appropriate proxies of local knowledge spillovers.