Quality and agronomic performance of 14 winter durum wheat genotypes (Gs) were examined in Austria, France and Hungary for 3 years. Heading time, wet gluten content, semolina yield and grain protein content are traits that showed G-dependent significant differences between the two management (M) systems examined (conventional and organic). Therefore, breeding for these traits could result in specifically adapted Gs for organic agriculture in different countries. Based on strong or moderately significant correlations between traits, gluten index and plant height could also be specifically selected in an indirect way. The need for environmentally specific selection for grain yield (GY) in later generations was also demonstrated. In general, varieties that had the highest performance in a given mega-environment (E) originated from that mega-E (except for yellow index). This finding provides evidence for the influence of the selection E, whether it is the M system or the growing region. As the French site fell into a distinct mega-E, it should be handled separately. The Hungarian site was found to be an ideal test E for selecting Gs with high adaptability for most of the quality traits, while the Austrian site could be used in selecting agronomic traits. This was also reflected in the breeding origin of the best winter durum Gs for each trait. Based on these findings, a partly separate winter durum selection program is recommended for organic and low input agriculture in each country. As a consequence, specific varieties adapted to sub-optimal growing conditions would support the emerging movement towards sustainable farming systems.