The integrated crop–livestock system (ICLS) is a farming strategy that helps to sustain agrobiodiversity, ecosystem services, and restores environmental sustainability. Furthermore, ICLS provides food and nutritional security to the small and marginal farmers in developing nations. In this context a mass-balanced ecosystem model was constructed for a smallholder ICLS along the Indian west coast to analyze the agro-ecological performance in terms of sustainability, resource use, nutrient balance and recycling. Thirteen functional groups were defined in the ICLS model with trophic levels ranging from 1.00 (detritus and benthic nitrogen fixers) to 3.00 (poultry and ruminants). The total system throughput index was estimated to be 1134.9 kg N ha⁻¹ year⁻¹ of which 60% was from consumption, 15% from exports, 10% from respiration, and the remaining 15% eventually flowing into detritus. The gross efficiency of the ecosystem was estimated to 0.3, which indicated higher growth rates and low maintenance energy costs. The higher food self-sufficiency ration of 7.4 indicated the integration of crop–livestock as an imperative system to meet the food and nutritional requirement of the farm family. The indices such as system overhead (60%), Finn’s cycling index (16.6) and mean path length (3.5) denoted that the ICLS is a small, resource-efficient, stable, maturing and sustainable ecosystem in terms of the ecosystem principles and recycling. The present model will serve as the first model on the ICLS from the humid tropics and will help in the evaluation of the other agro-ecological systems using the Ecopath modelling approach. In conclusion, farm intensification through crop and animal diversification has the highest impact on farm productivity, food self-sufficiency and resource-use-efficiency of the smallholder’s livelihood security.