The mechanism of Zr-BEA hydrothermal synthesis in fluoride media has been investigated through the detailed characterization of samples obtained at different synthesis times by XRD, XRF, TGA, multinuclear solid-state NMR, FTIR, SEM, TEM with EDS, XAS, and nitrogen sorption. The synthetic procedure involved hydrothermal crystallization of the gel with the following composition: 1SiO2:0.54TEAOH:0.54HF:0.005ZrO2:5.6H2O. The formation of open and closed Lewis acid sites was monitored by FTIR spectroscopy of adsorbed CO, while coordination of Zr was studied by XAS. The results show that the formation of Zr-BEA proceeds by two steps. In the first step, pure silica BEA is crystallized via a solid-solid hydrogel rearrangement mechanism. Zirconium species are occluded in Si-BEA crystals in the form of Zr-rich silicate particles. These particles do not provide for any appreciable Lewis acidity. In the second step, Zr incorporation into T positions of the zeolite structure takes place, leading to the formation of closed Zr sites, which are partially converted into open sites at longer synthesis times. It is demonstrated that the content of open and closed sites can be tuned by variation of the synthesis time.