Micronutrient malnutrition and suboptimal yields pose significant challenges in rainfed cropping systems worldwide. To address these issues, the implementation of climate-smart management strategies such as conservation agriculture (CA) and system intensification of millet cropping systems is crucial. In this study, we investigated the effects of different system intensification options, residue management, and contrasting tillage practices on pearl millet yield stability, biofortification, and the fatty acid profile of the pearl millet. ZT systems with intercropping of legumes (cluster bean, cowpea, and chickpea) significantly increased productivity (7–12.5%), micronutrient biofortification [Fe (12.5%), Zn (4.9–12.2%), Mn (3.1–6.7%), and Cu (8.3–16.7%)], protein content (2.2–9.9%), oil content (1.3%), and fatty acid profile of pearl millet grains compared to conventional tillage (CT)-based systems with sole cropping. The interactive effect of tillage, residue retention, and system intensification analyzed using GGE statistical analysis revealed that the best combination for achieving stable yields and micronutrient fortification was residue retention in both (wet and dry) seasons coupled with a ZT pearl millet + cowpea–mustard (both with and without barley intercropping) system. In conclusion, ZT combined with residue recycling and legume intercropping can be recommended as an effective approach to achieve stable yield levels and enhance the biofortification of pearl millet in rainfed agroecosystems of South Asia.