This study examined energy, greenhouse gas emission and ecological footprint analysis (EFA) of chickpea and lentil cultivation with different mechanization production systems. In lentil production, except for tillage operations, other operations are performed manually and the remaining straw is burned in the field; while in chickpea production, most of the agricultural operations are mechanized and residues are collected, baled and transferred to the warehouse for animal feed. In this paper, for the first time, some of the sustainability indicators are investigated and compared in two different legume production systems. Energy productivity and net energy for chickpea and lentil production were calculated at 0.036, 0.161 and 2373 and 5900 MJ per hectare, respectively. The CO2 emission and ecological carbon footprint were 173 kg CO2−eq and 0.15 global hectare for lentil and 484 and 0.87 for chickpea production. Totally, due to excessive consumption of diesel fuel and lack of proper management, the social cost of emission from straw baling in chickpea production (27.65 dollars per hectare) was higher than burning straw in lentil production (8.77). Multi-objective genetic algorithm results showed the potential of minimizing diesel fuel and fertilizer consumption and no chemical for chickpea production. Overall audition results of two different production systems revealed that traditional lentil production is more sustainable. Therefore, implementations of modern agricultural practices alone are not enough to achieve sustainability in agricultural production systems.