Consumers demand for healthier food and governments’ policies for environmental sustainability of agri-cultural processes are increasingly promoting a rapid expansion of organic farming. Nevertheless, the linkbetween organic products and their enhanced nutritional/environmental values is far from being fullyunderstood. In this context, we have begun to assess the effect of cultivation variables that may inter-act with farming systems and ultimately affect the final product quality. By comparing the response toconventional vs. organic farming of cauliflower, endive and zucchini here we demonstrate that the over-all quality of organic products depends on many interacting variables. In cauliflower, the cultivar effectoverwhelms other quality determinants with respect to antioxidant activity and nitrate accumulation.In endive, the liposoluble antioxidant activity increases under organic cultivation only in the absence ofmulching. Finally, organic farming promotes the accumulation of K in zucchini grown on clay but not onsandy soil. Therefore, understanding the functional links between cultivation variables and physiologicalresponses is essential to improve and standardize the quality of organic products.