Agricultural activities and agro-inputs, particularly chemical fertilizers, farmyard manure, pesticide, sewage sludge, plastic mulch, irrigation, etc., are the primary source of pollutants in farmlands. Agricultural land degradation has become a major concern as it poses a threat to crop productivity. In recent years, microbial-assisted phytoremediation has gained much attention as a promising in situ remediation technology for cleaning polluted soils. Several beneficial rhizobacteria and endophytes facilitate phytoremediation by stimulating innate plant growth-promoting traits such as the production of siderophores, phytohormones, and chelators in addition to their ability to biodegrade contaminants and enhance their removal. Current studies on microbial mediated phytoremediation are demonstrating significant remediation potential. However, there are several challenges in the field that restrict the remediation process. Here we highlight the specific traits, mechanisms, roles, advantages, and problems associated with microbial-assisted phytoremediation.