Sustainable agriculture aims to meet the needs of the present without compromising the ability of future generations to meet their own needs. Microorganisms, especially soil microbes, play a pivotal role in achieving this goal by enhancing soil fertility, promoting plant growth, suppressing pathogens and aiding in biogeochemical cycling. This chapter explores the types of beneficial microbes, their mechanisms of action and their application in sustainable farming practices. The integration of microbial solutions into agricultural systems holds immense potential to reduce chemical dependency, mitigate environmental degradation, and enhance long-term productivity. The growing demand for sustainable agriculture has highlighted the vital role of microorganisms in improving soil fertility, enhancing crop productivity, and reducing dependence on chemical inputs. Microorganisms such as nitrogen-fixing bacteria, phosphate-solubilizing microbes, mycorrhizal fungi, and plant growth-promoting rhizobacteria (PGPR) contribute significantly to nutrient cycling, pest management, and stress tolerance in crops. Their application through biofertilizers and biopesticides promotes eco-friendly practices that align with environmental and human health goals. This chapter explores the diversity of beneficial microbes, their mechanisms of action, applications in sustainable farming, and innovations such as microbial consortia, genome editing, and microbiome engineering. It also addresses the current challenges in field efficacy, formulation stability, and regulatory support. With the integration of biotechnology, nanotechnology, and digital tools, the future of microbial-based agriculture offers promising avenues for resilient and climate-smart farming systems. Thus, microorganisms are emerging as cornerstone agents in achieving global sustainable agriculture goals.