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The applications of nanomaterial-based enzyme-mimics (Enz-Ms) in biocatalytically therapeutic and diagnostic fields have attracted extensive attention. The regulation of the biocatalytic performances and biofunctionalities of Enz-Ms are essential research objectives, including the rational design and synthesis of Enz-Ms with desired biofunctional molecules and nanostructures, especially at the level of molecules and even single atoms. Here, this timely progress report provides pivotal advances and comments on recent researches on engineering biofunctional Enz-Ms (BF/Enz-Ms), particularly chemical synthesis, functionalization strategies, and integration of diverse enzyme-mimetic catalytic activities of BF/Enz-Ms. First, the definitions and catalogs of BF/Enz-Ms are briefly introduced. Then, detailed comments and discussions are provided on the fabrication protocols, biocatalytic properties, and therapeutic/diagnostic applications of engineered BF/Enz-Ms via hydrogels, nanogels, metal–organic frameworks, metal–polyphenol networks, covalent–organic frameworks, functional cell membranes, bioactive molecules and polymers, and composites. Finally, the future perspectives and challenges on BF/Enz-Ms are outlined and thoroughly discussed. It is believed that this progress report will give a chemical and material overview on the state-of-the-art designing principles of BF/Enz-Ms, thus further promoting their future developments and prosperities for a wide range of applications.