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Rapid urbanization and industrialization have resulted in the generation of huge amount of heavy metals-laden wastewater in the recent era. Industries, such as pulp paper, distillery, tannery, textile, etc. produce hazardous wastewater which is directly affecting the environment and human health if disposed off without any treatment. Wastewater treatment is an expensive and energy-intensive procedure not only because of the massive concentrations of pollutants but also because of its large volume. Microbes are immune to the toxicity of metals and play an important role in the ecosystem's resource cycle and energy flow. As the introduction of microbes in detoxifying wastewater has proved to be a boon for the society and hence the emphasis is put on biomineralization, oxidation-reduction, bioprecipitation, bioaccumulation, biosurfactant technology, bioleaching, biovolatilization, and biosorption processes with their selective advantages and disadvantages. Heavy metals can be compartmentalized by microbial strains, such as Corynebacterium glutamicum (Pb, Zn, Cd, Co, Cr), Aspergillus lentulus (Cr, Cu, and Pb), Bacillus, Microbacterium, Micrococcus, Shinella, Arthrobacter, Bacillus, and Serratia. Nanocomposites (CuFeO, FeO, Co3O4@SiO2, Fe3O4 etc) being unique in nature helped the researchers in treating wastewater efficiently. Hence, this review was aimed to address the treatment of wastewater by removing the heavy metals employing microbes in combination with magnetic nanocomposites. The effect of heavy metals on biodiversity, role of microbiota in the environment for detoxification, and appropriate markers that represent the efficiency of removal of the metals from industrial wastewater have also been explored in this review. Furthermore, the issues that need to be addressed in the future, and significant points for further research are also highlighted.