Soil bioremediation is a process of using microorganisms to clean-up contaminated soil, while soil stabilization is an approach to adding materials to the soil to improve its physical properties and stability. In recent past, utilization of microbial enzymes appears to be one of the alternative and effective approaches in biodegradation for various complex and toxic environmental contaminants. Bio-enzymes seem to be involved in various aspects of soil bioremediation and plant–microbe interactions suggesting understanding the role of bio-Enzymes in soil ecosystems can help in designing more effective strategies for the removal of the contaminants from the environments. In this Chapter, we summarize the current knowledge on the biotransformations of toxic pollutants using novel omics approaches. This chapter presents an extensive exploration of bio-enzymes, unveiling their complexities and showcasing their tremendous potential in biocatalysis and diverse industries. This chapter, we will also focus on the current state of the art of biodegraded and toxic pollutants, focusing on the use of novel omics approaches (genomics, transcriptomics, proteomics, metabolomics, and fluxomics) as tools to study the molecular mechanisms behind the transformations of the toxic pollutants. By studying bio-enzymes, scientists can access their powerful capacities to promote healthcare and bioremediation, among several other fields.