In the last decade, mesoporous hydroxyapatite (HA) materials have received much attention regarding environmental applications (including adsorption of soil and water contaminants, films for lithium batteries, catalysts, and support systems for catalysis) and open up ample opportunities regarding biomedical devices and structures. Molybdenum ions may strongly influence catalytic and sorption properties of materials. The present study shows an influence of hydrothermal-synthesis conditions (including temperature and duration of the treatment) on phase composition, textural properties, and morphology of molybdate-containing HA. Powders with high crystallinity manifested Brunauer–Emmett–Teller specific surface area up to 55 m2/g with a pore volume of 0.33 cm3/g. The molybdate-containing HA powders were investigated by chemical analysis, X-ray diffraction, Fourier-transform IR spectroscopy, and transmission electron microscopy. Their specific surface area, pore volume, and pore size distributions were determined by low-temperature nitrogen adsorption measurements, zeta potential was quantified, and electron paramagnetic resonance spectroscopy was performed. The concentration of MoO42− preserving the one-phase state was found, and the impact of hydrothermal treatment mode was analyzed by machine learning using artificial neural networks.