Soil degradation and low productivity in semi-arid regions necessitate sustainable practices to enhance agroecosystem resilience. Limited research has examined the combined effects of tillage, intercropping, and nitrogen fertilization on soil carbon stock (SC) in semi-arid regions like Iran. This study fills this gap by aiming to optimize biomass production and improve soil health. A factorial experiment was conducted to evaluate three tillage systems (conventional, minimum, no-tillage), five planting patterns (sole triticale, sole hairy vetch, and inter-cropping ratios of 67:33, 50:50, 33:67), and three nitrogen levels (0, 60, 120 kg/ha). Soil samples from 0-30 cm depth were analyzed to assess SC and soil health. Conventional tillage with 60 kg/ha nitrogen increased aboveground biomass by 16.03% and total biomass by 28% compared to no nitrogen, driven by enhanced nutrient availability in sole triticale. No-tillage with 60 kg/ha nitrogen boosted below-ground biomass by 29.62%, total organic carbon by 45.03%, soil organic matter by 45.03%, total soil nitrogen by 45.11%, and SC by 57.41% relative to conventional tillage, due to minimal soil disturbance and residue retention. Intercropping, particularly the 67:33 ratio, improved SC by 15-20% and achieved land equivalent ratios above 1, reflecting efficient resource use. Net primary production under conventional tillage with 60 kg/ha nitrogen rose by 11.29% for plants and 11.18% for soil compared to no nitrogen. This study provides novel evidence that no-tillage, moderate nitrogen, and triticale-hairy vetch intercropping enhance soil health and CS in semi-arid agroecosystems, offering scalable practices for farmers to mitigate climate change and ensure sustainable productivity.