Assessing the energy cycle and greenhouse gas (GHG) emissions of wheat production in small Egyptian farms is essential to improve wheat productivity to meet population growth and achieve sustainable development. This study aims to compare wheat production in terms of energy use and GHG emissions for different scenarios in the Delta of Egypt and to use Data Envelopment Analysis (DEA) to optimize the wheat production system. Three common scenarios of the wheat production system (S-I, S-II, and S-III) from old lands with one scenario (S-IV) from newly reclaimed land were included in the study. Data were collected from small farmers through a face-to-face questionnaire and interviews in 2022–2023. The results showed that the third scenario (S-III) in the old lands had the lowest input energy consumption (42,555 MJ ha−1) and the highest output energy (160,418 MJ ha−1), with an energy use efficiency of 3.770. In comparison, the input and output energy for the newly reclaimed scenario (S-IV) were 37,575 and 130,581 MJ ha−1, respectively, with an energy use efficiency of 3.475. S-III was an optimum scenario due to its high energy indicators, such as energy productivity of 0.173 kg MJ−1. The total GHG emissions of S-III were the lowest in old lands with a value of 1432.9 kg CO2-eq ha−1, while S-IV had 1290.2 kg CO2-eq ha−1. The highest GHG emissions input was diesel fuel for machinery and irrigation, followed by manure, chemical fertilizers, and agricultural machinery use. Using mechanization in most farming operations for S-III and S-IV led to decreased losses of agricultural inputs with increasing outputs (yield and straw). Therefore, using them in wheat farming practices is recommended to increase the wheat farming system’s energy efficiency and GHG emissions.