Chickpea is a key crop in sustainable cropping systems and for its nutritional value. Studies on agronomic and genetic influences on chickpea protein composition are missing. In order to obtain a deep insight into the genetic response of chickpeas to management in relation to agronomic and quality traits, a two-year field trial was carried out with eight chickpea genotypes under an organic and conventional cropping system. Protein composition was assessed by SDS-PAGE in relation to the main fractions (vicilin, convicilin, legumin, lectin, 2s-albumin). Crop response was highly influenced by year and presumably also by management, with a −50% decrease in grain yield under organic farming, mainly due to a reduction in seed number per m2. No effect of crop management was observed on protein content, despite significant differences in terms of protein composition. The ratio between the major globulins, 7s vicilin and 11s legumin, showed a negative relationship with grain yield and was found to be higher under organic farming. Among genotypes, black-seed Nero Senise was characterized by the highest productivity and water-holding capacity, associated with low lectin content. These findings highlight the importance of the choice of chickpea genotypes for cultivation under organic farming in relation to both agronomic performance and technological and health quality.