In order to develop sustainable production of greenhouse crops, the economic, energy, and environmental aspects of production should be considered. The purpose of this study was to evaluate the economic, energy, and environmental (3E) sustainability of cucumber, tomato, and bell pepper production in greenhouses by performing material flow cost accounting (MFCA) and life cycle assessment (LCA) material and methods. Calculating the economic and energy value of losses in agricultural sustainability assessment studies is not common. Using the LCA method alone does not allow us to calculate the monetary and energy value of waste. If this method is used simultaneously with MFCA, this gap will be filled. The system boundary for LCA was from cradle to farm, and for MFCA, foreground processes were considered. The production of each crop was compared at the level of 1000 m2 during 1 year. Data were collected through questionnaire-based interviews. The gross value of production for cucumber, tomato, and bell pepper were 8982, 16387, and 17610 $/1000 m2, respectively. The negative production of cucumber, tomato, and bell pepper were 702, 718, and 449 $/1000 m2, respectively. The benefit-to-cost ratio in the production of cucumber, tomato, and bell pepper was calculated as 2.8, 5.17, and 5.8, respectively. The economic productivity in the production of cucumber, tomato, and bell pepper was calculated at 10.25, 7, and 4.4 kg/$. Labor cost was the main cost in the production of all three crops. The total input energy for the production of cucumber, tomato, and bell pepper was estimated to be 99.4, 123.1, and 164.6 GJ/1000 m2, respectively. Negative products in the production of cucumber, tomato, and bell pepper were obtained at − 24.2, − 23.9, and − 13.5 GJ/1000 m2, respectively. The energy productivity of cucumber, tomato, and bell pepper was calculated as 0.23, 0.26, and 0.08 kg/MJ, respectively. The specific energy indices were 4.32, 3.79, and 12.20 MJ/kg for cucumber, tomato,
