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Zr(IV)-based metal–organic frameworks (MOFs) such as the Zr(IV) trimesate MOF-808 are promising materials for catalytic applications. In this work, we report an aqueous solution-based room-temperature strategy to produce well-defined monodispersed MOF-808 nanocrystals down to 35 nm with a high space-time yield, up to 2516 kg/m3/day, and excellent crystallinity and porosity. The resulting nanocrystals show remarkable colloidal dispersion during 1 day in a wide range of nanoparticle concentrations. As a result, 35 nm MOF-808 colloidal-level nanocrystals exhibit the highest rate of selective peptide bond and protein hydrolysis among the reported Zr(IV)-based MOFs. This result may open new opportunities for highly efficient peptide or protein hydrolysis using scalable nanocatalysts.