Bioorthogonal chemistry introduces nonbiogenic reactions that can be performed in biological systems, allowing for the localized release of therapeutic agents. Bioorthogonal catalysts can amplify uncaging reactions for the in situ generation of therapeutics. Embedding these catalysts into a polymeric nanoscaffold can protect and modulate the catalytic activity, improving the performance of the resulting bioorthogonal “polyzymes”. Catalysts based on nontoxic metals such as gold(I) are particularly attractive for therapeutic applications. Herein, we optimized the structural components of a metal catalyst to develop an efficient gold(I)-based polyzyme. Tailoring the ligand structure of gold phosphine-based complexes, we improved the affinity between the metal complex and polymer scaffold, resulting in enhanced encapsulation efficiency and catalytic rate of the polyzyme. Our findings show the dependence of the overall polyzyme properties on the structural properties of the encapsulated metal complex.