Pearl millet stands as an important staple food and feed for arid and semi-arid regions of India and South Africa. It is also a quick supplier of important micronutrients like Fe and Zn via grain to combat micronutrient deficiencies among people in developing countries. India has notably spearheaded advancements in pearl millet production and productivity through the All India Coordinated Pearl Millet Improvement Project. There were 21 hybrids evaluated over arid and semi-arid ecologies of the western and southern regions of India. AMMI and GGE biplot models were adopted to recommend a specific hybrid for the particular locality. A joint analysis of variation indicated a significant genotype–environment interaction for most of the agronomical and grain micronutrient parameters. Pearson’s correlation values dissected the significant and positive correlation among agronomic traits and the negative correlation with grain micronutrient traits. GGE biplot analysis recommended the SHT 106 as a dual-purpose hybrid and SHT 115 as a biofortified hybrid for the grain’s Fe and Zn content. SHT 110 and SHT 108 were selected as stable and high grain yield-producing hybrids across all environments and specifically for E1, E2, and E4 as per the Which-Won-Where and What biplot. SHT 109 and SHT 103 hybrids were stable and high dry fodder yield-producing hybrids across all environments. In this study, the Multi-Trait Stability Index (MTSI) was employed to select the most stable and high-performing hybrids for all traits. It selected SHT 120, SHT 106, and SHT 104 for stability and great performance across all environments. These findings underscored the significance of tailored hybrid recommendations and the potential of pearl millet in addressing both food security and malnutrition challenges in various agro-ecological regions.