Bioorthogonal chemistry has emerged as a promising strategy for regulating bioprocesses through abiotic reactions. Bioorthogonal unmasking reactions mediated by transition metal catalysts (TMCs) present a powerful tool for biomedical applications due to their ability to generate therapeutic agents in situ, minimizing off-target effects. However, the direct application of TMC-mediated reactions in a biological environment poses challenges due to limited water solubility and biocompatibility of these catalysts. My Ph.D. research focused on encapsulating TMCs into polymer nanoparticles to obtain bioorthogonal nanocatalysts. These nanoscaffolds solubilize and stabilize hydrophobic catalyst molecules while preserving catalytic activity and stability in complex biological media. Furthermore, by varying their structure design and/or formulation strategies, these nanocatalysts provided enhanced biocompatibility while enabling controlled drug release for imaging and therapeutic applications.