Agriculture in India accounts for 18% of greenhouse gas (GHG) emissions and uses significant land and water. Various socioeconomic factors and food subsidies influence diets in India. Indian food systems face the challenge of sustainably nourishing the 1.3 billion population. However, existing studies focus on a few food system components, and holistic analysis is still missing. We identify Indian food systems covering six food system components: food consumption, production, processing, policy, environmental footprints, and socioeconomic factors from the latest Indian household consumer expenditure survey. We identify 10 Indian food systems using k-means cluster analysis on 15 food system indicators belonging to the six components. Based on the major source of calorie intake, we classify the ten food systems into production-based (3), subsidy-based (3), and market-based (4) food systems. Home-produced and subsidized food contribute up to 2000 kcal/consumer unit (CU)/day and 1651 kcal/CU/day, respectively, in these food systems. The calorie intake of 2158 to 3530 kcal/CU/day in the food systems reveals issues of malnutrition in India. Environmental footprints are commensurate with calorie intake in the food systems. Embodied GHG, land footprint, and water footprint estimates range from 1.30 to 2.19 kg CO2eq/CU/day, 3.89 to 6.04 m2/CU/day, and 2.02 to 3.16 m3/CU/day, respectively. Our study provides a holistic understanding of Indian food systems for targeted nutritional interventions on household malnutrition in India while also protecting planetary health.