The food industry is the most important industrial activity in Spain in terms of production and employment; its spatial concentration is considerable. However, there is a lack of quantitative research on its agglomerations, especially at high levels of spatial and sectorial disaggregation. With the study presented, this deficit is addressed, using systematic and quantitative methods to examine the spatial agglomeration in the subsectors that the food industry is specialized. Spanish food industry clusters have been identified by applying a top-down quantitative methodological approach—the cluster index—and following a high level of territorial and sectorial disaggregation. Clusters were identified at the three- and four-digit sectorial disaggregation. The number of four-digit-level relevant clusters was higher than three-digit disaggregation. This evidence was verified using nonparametric statistical tests (Wilcoxon signed-rank test). Furthermore, the analysis of four significant three-digit subsectors allows us to advance two alternative explanations for the divergent results at the different levels of the analysis (three digits vs. four digits). This partly explains the potential competitiveness of Spain in the food industry and shows the possibility of establishing policies for the development of clusters.