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The agrarian communities of South Asia are dominated by small and marginal farmers (<2.0 ha operational holdings) and are confronted with manifold challenges of lower productivity, income, and resource degradation. For optimized and efficient resource use, a shift from business as usual towards green economy is imperative. Therefore, a study to address these challenges, through integrating diverse crops and allied enterprises under an integrated farming system (IFS) model was carried out. We hypothesized that a standardized IFS model with appropriate location-specific modules will have higher system output, income, and lesser environmental footprints. Vegetable cultivation (VC), protected vegetable cultivation (PVC), field crops (FC), mushroom production (MP), and beekeeping (BK) were evaluated under the IFS model, with objectives to optimize the coherent use of available farm resources with enhancing system productivity and profitability. Among the FC module, the system productivity increased from 21–247% of different cropping systems, over the predominant rice–wheat system (RWS). The integration of different components, viz., VP + PVC + FC + AHS + MP + BK + VC in M₁₀ resulted in achieving the maximum water productivity (6.72 kg/m³), energy productivity (1.50 kg/MJ), net return (9446 USD/ha), employment opportunities (792 man-days), sustainable livelihood index (70.2%), and nutrient cycling (138.12, 67.9, and 381.6 kg/ha of nitrogen, phosphorus, and potassium, respectively). These findings can be a scientific basis for the optimization and sustainable management of natural resources under different modules of IFS for the less-endowed small and marginal farmers.