Microbial enzymes have immense applications in the pharmaceutical industry, due to their advantages over chemical alternatives being environmentally friendly, high specificity and efficiency, and ability to function under extreme conditions. These enzymes are extensively utilized in the pharmaceutical sector for enzyme replacement therapy (ERT) and as alternative therapeutics for various conditions, including cancer, metabolic disorders, and inflammatory conditions. The applications of these enzymes include diagnosis as well as treatments such as lipases for chiral drug synthesis, proteases for anti-inflammatory agents, asparaginase for leukemia treatment. In addition to this, microbial enzymes also have been explored as thrombolytic and digestive agents. This chapter provides an overview of the current status and future scope of microbial enzymes in pharmaceutical applications while acknowledging challenges such as immunogenicity, tissue specificity, and others.