Reducing waste is a significant strategy for reducing the negative environmental effects of agricultural production. Material flow cost accounting (MFCA) is an environmental management tool that can assist farmers to better understand the financial and environmental consequences of the use of materials and energy and provide opportunities for achieving financial and environmental sustainability of agricultural activities by providing solutions. The objective of MFCA for soybean production is to quantify and identify agricultural inputs/energy waste to improve management of residue, waste and energy at different stages of crop production. Analysis of the economic and environmental performance of soybean production was performed using an MFCA for the first time. Current economic and cost analysis using MFCA was compared and a new method was used for incorporating material waste into classic energy and cost analysis. The results shows that the total energy consumption and production cost for 2701 kg of soybean seed were 52064.63 MJ and 1408 USD, respectively. The economic indices of gross production value, gross return and the benefit/cost ratio were evaluated for conventional and MFCA cases. The MFCA results indicate that gross production value, gross return and the benefit/cost ratio were 2103 USD ha−1 and 695 USD ha−1 and 1.49, respectively. These values for conventional calculations were 1781 and 373 USD ha−1 and 1.26, respectively. The gross income in conventional mode showed a difference of 322 USD with MFCA, which is equivalent to the cost of material waste. The benefit/cost ratio was higher by 0.22 because of the calculation of the cost of material waste in MFCA. The efficiency of the use of energy and energy productivity were calculated based on the equivalent input and output energy. The energy use efficiency of soybean production in MFCA-based and conventional calculations were 1.04 and 1.29, respectively. In this case, energy use efficiency decreased by 0.2
