Rising micronutrient deficiencies pose a significant threat to the well-being of preschoolers in Madagascar. The lack of effective interventions to improve their nutritional status further exacerbates this issue. A comprehensive study was conducted to investigate the complex relationship between agriculture, food/nutrition security, and the nutritional status of children, using a dual approach (the dietary diversity and the micronutrient intake approach). To unravel the intricate connections, a 3-year panel dataset was used. The results of the study provide compelling evidence supporting the link between production diversity and dietary diversity, and its positive association with children’s weight. Furthermore, the study reveals that pulse production has a direct association with increased energy and micronutrient intake, particularly zinc intake. Another noteworthy finding from the study is the positive correlation between zinc intake and the reduction of undernourished and stunted children. Zinc, an essential micronutrient, thus plays a vital role in child growth and development. By emphasizing the importance of zinc-rich foods and supporting its production, policymakers can work toward mitigating the nutritional challenges faced by these vulnerable populations, ultimately contributing to the well-being and development of preschool-aged children.