By combining in situ X‐ray diffraction, Zr K‐edge X‐ray absorption spectroscopy and 1H and 13C nuclear magnetic resonance (NMR) spectroscopy, we show that the properties of the final MOF are influenced by H2O and HCl via affecting the nucleation and crystal growth at the molecular level. The nucleation implies hydrolysis of monomeric zirconium chloride complexes into zirconium‐oxo species, and this process is promoted by H2O and inhibited by HCl, allowing to control crystal size by adjusting H2O/Zr and HCl/Zr ratios. The rate‐determining step of crystal growth is represented by the condensation of monomeric and oligomeric zirconium‐oxo species into clusters, or nodes, with the structure identical to that in secondary building units (SBU) of UiO‐66 framework. The rapid crystallization in the absence of HCl leads to formation of defective secondary building units with missing zirconium atoms, providing a pathway to control the number of defects in UiO‐66 crystals. Remarkably, we have shown that assembling of the metal nodes and linkers into the UiO‐66 structure is not the rate‐limiting step, and the degree of deprotonation of the linker has no direct effect on the crystallization kinetics or crystal size of product.
