The authors examine the differences in the behavior of the innovation between the Spanish agrifood and manufacturing firms using firm‐level data from 1990–2008 to analyze the persistence in innovation and to explore the explanatory determinants of the probability of being product and process innovator. Survival functions, transition probability matrices, and dynamic discrete choice panel data models are combined to measure persistence. The results suggest that in the food industry the persistence of process innovation is higher than in product innovation. Environmental and market determinants such as market changes or appropriability are more decisive to explain innovation in food industry. By contrast, several determinant variables for innovation activities in the manufacturing sector seem not to be linked with the innovation in food firms. That is the case of the outsourcing ratio and the positive evolution of market share of the individual firm.