Arbuscular mycorrhizal fungi (AMF) and Lactobacillus plantarum (LP) play pivotal roles in plant salinity resistance; however, difficulties are still exist in ascertaining their synergistic effects in counteracting legume soil salinity. Here, two peanut cultivars (salt‐tolerant and salt‐sensitive) were subjected to salinity stress, and the alleviation effects of combined microbial agent (CMA, inoculation with AMF + application with LP) on peanut salinity tolerance have been comprehensively characterized. CMA significantly enhanced the biomass production, leaf relative water content, increased the net photosynthetic rate, the maximal photochemical efficiency of photosystem II (PSII) and strengthened the antioxidant system, while dramatically decreased the reactive oxygen species (ROS) accumulation, lipid peroxidation and relative electrolyte conductivity under salinity conditions. Moreover, transcriptional and metabolomic evidence advocated that a subset of stress‐responsive pathways involved in plant growth (e.g. sucrose and starch), photosystem, antioxidant response, signal transduction (e.g. phytohormone and MAPK), osmotic homeostasis (e.g. total soluble sugar and amino acids) and root metabolism (e.g. asparagine and phenylpropanoid) have been regulated by CMA. Taken together, the physiological, transcriptional and metabolomic results indicate that CMA could induce peanut salinity tolerance through increasing plant growth performance, maintaining photosynthetic apparatus integrity, enhancing antioxidant system and regulating root metabolism. This study provides a promising CMA product and would be important for deepening the knowledge of the mechanisms regarding bacterial–fungal interactions.