The pioneering hydrothermal synthesis of the compound Be2[(Si1−xGex)O4] with a phenakite structure (the size of individual crystals up to 1 mm) was carried out in acidic alkaline-containing fluoride solutions at a temperature of 625 °C and a pressure of ~ 150 MPa. Uniform (x = 0, 0.80 and 1) and zonal (x = 0.04 − 0.025) Be2[(Si1−xGex)O4] crystals synthesized in the Li-containing mineralizer were obtained. The possibility of formation of intermediate compounds under hydrothermal conditions remains an open question. In the Na-containing mineralizer, only Be2SiO4 crystallizes due to the formation of insoluble sodium germanates. The fading of formation of Be2[(Si1−xGex)O4] was determined with the use of technique of temperature-induced zoning and can be explained by the fact that newly formed crystals screen the surface of the initial BeO. The instantaneous growth rates of the prismatic faces of Ge-substituted phenakite crystals, decreasing from 18 microns/day to 2, were determined using the technique of temperature-induced zonality. The crystal structures of Be2[(Si1−xGex)O4] samples with x = 0, 0.80 and 1 were refined by direct X-ray diffraction methods, and the linear dependence of the unit cell parameters and bond lengths on the germanium content has been quantitively described. First Raman spectroscopy study of Be2[(Si1−xGex)O4] on zonal crystals indicated the linear shift of vibration bands in Raman spectra to a lower frequencies with an increase in germanium concentration (x up to 0.25). A new Raman band of Ge–O stretching vibrations at ~ 1115 cm−1, which is not common for natural and synthetic germanium-free phenakites, was observed.