Green cucumber named Cucumis sativus is one of the most important vegetables. Currently, it has the highest level of cultivation in greenhouses in the country. To increase yields, greenhouse managers use chemical fertilizers at different stages of plant development, which upset the balance of the environment and the soil microbiome. Using growth-promoting bacteria, in addition to maintaining the balance of soil microorganisms, can improve crop quality. In this study, the effects of two bacterial strains of Amycolatopsis sp. strain 1119 and Pseudomonas sp. strain P3-57 on soil microbial population, production rate, and crop quality in commercial cucumber greenhouse were investigated. The use of P3-57 and 1119 strains increased the yield by 4% and 23%, respectively. Qualitative evaluation of the product revealed that both bacteria had a favorable effect on the overall acceptance of the product. Examination of the growth-promoting colonization bacteria showed that strain 1119 is an endophytic bacteria and strain P3-57 colonized on the root. The 1119 strain increased the number of cultivable fungi in the rhizosphere and decreased the number of bacteria. Treatment with strain P3-57 increased the population of both groups of microorganisms. Using these bacteria in the industry can significantly help protect the environment in the future.