Ever since the start of the Industrial Revolution, environmental pollution has significantly increased. The prominent cause of most diseases in humans, animals, and plants is the presence of toxic materials, pollutants, contaminants, and hazardous compounds released by industries. One of the major factors is the presence of heavy metals in the air, water bodies and soil. Heavy metals have biomagnification and bioaccumulation characteristics, making them hazardous for flora and fauna on a large scale. Recently, biological sources such as bacteria, fungi, algae, etc., have been used to bioabsorb these heavy metals. The microbial properties of these cell walls are utilized for effective and low-cost absorption of metals. Bioaugmentation, biosorption and biostimulation are effective strategies for reducing the toxicity of hazardous contaminants in the soil and facilitating bioremediation. The mechanism of biosorption is mainly based on ions and functional groups present in the microbes. Fungal species are advantageous over bacteria as they are easier to handle, cost-effective and, most importantly, non-pathogenic, making them ideal candidates for biosorption. This review provides a comprehensive overview of various microbial strains utilized in bioremediation. Further, the review highlights the application of nanotechnology and metabolic engineering approaches to improve the efficacy of Biosorption, Biostimulation and Bioaugmentation. It provides insights on the role of microbial nanoparticles in bioremediation and prospects in the forte of microbe-assisted bioremediation.