While patterning the nucleation of crystalline inorganics at the nanometer length scale via low temperature, aqueous growth methods is highly desirable, it remains synthetically challenging. We report a generalizable approach for fabricating crystalline nanostructured inorganics at temperatures below 60 °C with periodicities on the order of 50 nm. A block copolymer (BCP) of polystyrene-block-poly[(allyl glycidyl ether)-co-(ethylene oxide)] (PS-b-P(AGE-co-EO)) is used to prepare periodically ordered, reactive thin film templates that are functionalized postassembly with an amino acid, cysteine, via thiol–ene click chemistry, exclusively at the sites of the exposed P(AGE-co-EO) domains. These functionalized areas subsequently template the confined crystallization of copper(I) oxide (Cu2O) and zinc oxide (ZnO) with high fidelity, from aqueous solutions at low temperatures. The demonstrated method provides a versatile materials platform to control the growth of nanostructured crystalline materials via the introduction of a plethora of surface functional groups by means of facile thiol–ene click chemistry. The resulting organic substrates can be used to template the growth of multiple different crystalline inorganic materials on surfaces nanostructured via BCP self-assembly.