Zeolitic imidazolate frameworks (ZIF-8) have promising applications as sensors or catalysts due to their highly porous crystalline structures. While most of the previous studies are based on ZIF-8 crystals either in isolated particles in aqueous environments or in a compact colloidal form, here a facile method is reported to achieve wafer-based isolated ZIF-8 nanocrystals to facilitate their integration in microsystems and as surface coatings for catalysis. The fabrication process includes the growth of compact zinc oxide film by atomic layer deposition that functions as the Zn source for the ZIF-8 synthesis, and the dispersion of gold nanoparticles as inhibitors for the following crystallization transformation of ZIF-8 crystals. By choosing the concentration of gold nanoparticles, the density of ZIF-8 nanocrystals can be controlled and the sizes of individual ZIF-8 crystals can be scaled down to ≈100 nm. A wide range of structural colors generated by the ZIF-8 nanocrystals is also observed, which can be attributed to the size-dependent resonant scattering as verified by finite-difference time-domain simulations and classical Mie theory. The scalable fabrication of wafer-based ZIF-8 nanocrystals empowered with tunable optical properties paves a new way to explore the promising applications in nanophotonics and bionanotechnology.