The conventional agricultural production systems are facing multiple challenges of yield plateauing, low farm profitability, energy intensiveness, unemployment, and environmental unsustainability. Hence, four production scenarios viz., integrated organic management, integrated crop management, conservation agriculture, and conventional system and three cropping system viz., maize-mustard, maize + cowpea-mustard, and pigeon pea-wheat were tested to examine their energy, carbon, and economic feasibility for the development of environmentally clean production system. The integrated crop management system recorded significantly higher system productivity (12621 kg ha⁻¹), net energy (471632 MJ ha⁻¹), and economic returns (US$ 2079 ha⁻¹). However, the integrated organic management system resulted in the highest energy productivity (0.83 kg MJ⁻¹), eco-efficiency (0.18 US$ MJ⁻¹ha⁻¹), carbon economic efficiency (2.47 US$ ha⁻¹CO2-eq), and carbon sustainability index (37.5), and the lowest greenhouse gas intensity (0.06 kg grain kg⁻¹CO2eq). Among the cropping systems, maize + cowpea-mustard produced 32.6% higher net energy and 31.1% higher energy use efficiency over the maize-mustard system, respectively. However, the pigeonpea –wheat system recorded the highest carbon economic efficiency (1.41 US$ kg⁻¹ CO2eq), and carbon sustainability index (24.4). The greenhouse gases intensity was positively (+) correlated with specific energy but negatively (-) correlated with carbon ecological efficiency, C-gain, and carbon sustainability index. Thus, the study suggested that the intensified cropping is profitable and environmentally clean systems either in integrated crop management or in integrated organic management scenarios.