Chemical input reduction in agricultural systems is strongly demanded with the aim to improve the quality and the safety of food/feed products in an environmental sustainable perspective. Durum wheat is the most important food crop widely grown across the Mediterranean basin. However, the choice of tailored-genotypes can represent a key strategy in resource limiting conditions. The present study investigated the performance of fourteen commercial durum wheat varieties, in terms of morphologic, productive and quality traits under two cropping systems, conventional (CH) and no-chemical input (NC), for two growing seasons. The NC cropping system affected plant phenology, grain yield, and its components (i.e., ears m−2 and test weight). However, the negative influence exerted by the NC depended by the growing season (significant interaction between growing season and cropping system), which in turn affected the production behavior of genotypes (significant interaction between growing season and genotype). The additive main effect and multiplicative interaction (AMMI) analysis showed that genotype (G) effect explained the 4.3% of the total variability, the environment (E) the 71.7% and the G × E interaction the 9.4%. The AMMI stability value (ASV) indicated that Meridiano, Claudio, Saragolla, and Normanno were the most stable genotypes among environments (combination of years and management systems). An integrated environmental assessment, including a soil nitrogen balance, can help to provide a more holistic approach to the sustainability of the no-chemical Mediterranean cropping systems based on cereal-legume rotation.