<p>Hidden hunger remains a major public health challenge in India, yet it has not received the attention it deserves in research and policy. Despite significant progress in food production, micronutrient deficiencies continue to affect large sections of the population, particularly in rural areas. This study investigates the spatial association between agricultural diversity and nutrient deficiency at the district level across India, addressing a critical evidence gap in understanding how cropping patterns influence nutritional outcomes. Using data from NSS (2011–12) and employing the Small Area Estimation technique, we estimated the prevalence of protein, iron, and folate deficiencies at the district level, accounting for sampling variability and regional heterogeneity. Our analysis reveals that higher crop diversity is concentrated across western, central, and southern India, with prominent pockets in Rajasthan, Gujarat, Maharashtra, Karnataka, Andhra Pradesh, and Tamil Nadu, along with select districts in Madhya Pradesh, Telangana, Uttarakhand, and Himachal Pradesh. The spatial analysis identifies significant associations between agricultural diversity and nutrient deficiency. Districts with more diversified farming systems tend to exhibit lower levels of micronutrient deficiency, with protein, iron, and folate showing consistent High Low clustering across the western and central regions of India, including large parts of Rajasthan, Gujarat, Maharashtra, and Madhya Pradesh, along with smaller pockets in adjoining states. These findings highlight the crucial role of agricultural diversification in improving dietary quality and nutritional outcomes. The study underscores the need for region-specific agricultural policies and recommends the implementation of conditional incentive programs to promote crop diversification as a sustainable approach to combat micronutrient malnutrition in India.</p>