This paper analyzes innovation in firms using a Sectoral System of Innovation approach on the food processing sector in Argentina, Brazil and Chile. The principal component analysis performed using data from the World Bank Investment Climate Survey shows that firms’ knowledge bases have evolved largely through acquiring new equipment and foreign technology, while the embedding institutions have impeded rather than assisted innovation. The Probit estimation results confirm that only a few of the sectoral system of innovation variables have had a positive impact on innovation. Overall, the evidence shows that these countries should invest more on indigenous capabilities, thus effecting institutional change for facilitating innovation.