The degradation of soil characteristics caused by salinity and sodicity gives rise to severe limitations on crop production. Therefore, the current study was conducted in a split block design with three replicates during the winter (2019/2020) and summer (2020) seasons at Sakha Agriculture Research Station Farm, Kafr El-Sheikh Gov., Egypt to study the integrated effect of gypsum with mycorrhizae fungi inoculation to improve saline-sodic soil properties and bacterial communities, physiological and productivity of wheat and maize plants. The treatments included different soil gypsum levels (G0: none, G1: 7.5 Mg ha-1, and G2: 10 Mg ha-1) of the requirements and mycorrhizal fungi inoculation (without inoculationAMF0 and inoculated AMF1). The results showed that the combination of G2 + AMF1 caused significant changes in the photosynthetic activity, antioxidant enzyme activities (catalase, peroxidase and superoxide dismutase), mycorrhizal root colonization, total bacterial counts, P solubilizer bacteria, and respiration of microbial soil in the Rhizosphere of wheat and maize. In addition, after two growing seasons, electrical conductivity (EC) decreased from 7.09 to 4.57 dS m-1, exchangeable sodium percentage (ESP) from 19.35 to 15.47 and soil bulk density (BD) from 1.38 to 1.31 Mg m-3. While the exchangeable calcium percentage (ECaP) increased from 11.51 to 15.47, available phosphorus (Av. P) from 8.19 to 11.17 mg kg-1, infiltration rate (IR) from 0.7 to 0.97 cm hr-1, and total porosity (TP) from 47.92 to 50.44 % and G2 + AMF1 treatment gave the highest grain yield of wheat and maize were 7.72 and 8.52 Mg ha-1, respectively.