Considering future tasks in soil health, resources management and environmental protection, farmers are challenged to develop sustainable strategies for managing soil and land resources. In this study, the long-term sustainability of two fertilization strategies, - current, with synthetic fertilizers (SYN) vs conservative, with organic sources of nitrogen (organic amendments plus green manure with a legume - CONS) - was assessed in a processing tomato/durum wheat rotation. The EPIC model was used, validated with field data then run to simulate the management for 30 years under 3 current and future climates. Yield, soil organic carbon (SOC) stock change, nitrogen use efficiency (NUE), water use efficiency (WUE) and nitrate leaching were considered as sustainability indicators. Under all the future climate scenarios, tomato yield increased in CONS, remaining almost stable in SYN. Wheat yield increased both in CONS and SYN, but the average yield in CONS was considerably lower than in SYN. NUE and nitrate leaching followed the same trend, both decreasing in CONS, while WUE was higher in CONS compared to SYN. The effect of CONS on SOC was always positive. Thus, the alternative N fertilization strategy proposed can be a favorable option for maintaining soil health and a sustainable crop production.