<p>The widespread use of pesticides in modern agriculture has significantly boosted crop yields but also raised critical environmental and health concerns due to their persistence and toxic residues. While microbial biodegradation offers a promising solution, the environmental fate and behavior of pesticide degradation metabolites, particularly their solubility, mobility, and ecotoxicological risks, remain poorly understood. This review examines the dual role of microbial secondary metabolites in enhancing pesticide degradation while potentially exacerbating environmental contamination. On one hand, microbial biosurfactants (e.g., those produced by <i>Pseudomonas</i> and <i>Bacillus</i> spp.) and extracellular enzymes (hydrolases, oxidoreductases) increase pesticide solubility and breakdown efficiency. Fungal strains such as <i>Aspergillus niger</i> and <i>Penicillium chrysogenum</i> demonstrate remarkable degradation capabilities (&gt;85% for organophosphates), often outperforming bacterial systems. While biosurfactants and enzymes improve pesticide breakdown efficiency, the resulting degradation products, such as 3,5,6-trichloro-2-pyridinol (TCP) and malaoxon are often more mobile and ecotoxic. Despite advances in analytical techniques (e.g., GC-MS, LC-MS/MS) to track these metabolites, their long-term ecological impacts remain understudied. We argue that optimizing microbial consortia (combining biosurfactant producers with degraders) and prioritizing metabolite toxicity assessments are essential for sustainable bioremediation. This review bridges the gap between laboratory scale degradation studies and real-world environmental safety, urging a paradigm shift from mere pesticide removal to comprehensive risk management of transformation products.</p> Graphical Abstract <p></p>