Microorganisms can survive in a toxic environment by utilising carbon, phosphorous, sulfur, and nitrogen from the available sources thanks to their ability to detoxify xenobiotic substances. The most practical and efficient metabolic method for breaking down xenobiotic substances is biotransformation. Because of specific genes, enzymes, and degradative systems, microorganisms possess extraordinary abilities. Due to their special characteristics, microorganisms like bacteria and fungus can either fully or partially metabolize xenobiotic compounds in a variety of habitats. The molecular mechanisms of degradative processes and the routes to decontaminate or alter the fundamental structure of xenobiotics in nature can be understood using a variety of state-of-the-art techniques. These techniques look at new proteins, catabolic genes, and microbes along with their metabolic apparatus. In order to identify the catabolic genes, enzymes, and strategies involved in employing an environmentally friendly strategy to counter the threat posed by xenobiotic chemicals, this article discusses recent developments and current trends.