Chemical farming depends predominantly on the exhaustive claim of a variety of agrochemicals mainly mineral fertilizers and pesticides that deteriorated health and environmental ecosystems. On the other hand, clean farming systems applies novel agricultural biotechnology basically microbial inoculants to remediate polluted ecosystems, enhance plant growth, and suppress plant disease as well as reducing agrochemical uses and conserving biodiversity. Realizing the potential of beneficial microorganisms, they are now urgently needed to combat environmental and health adverse impacts of agrochemicals. This review focuses on the use of beneficial microbial inoculants to sustain farming systems