A soft chemistry approach was applied to synthesize de(sodiated) transition-metal hydroxy molybdates under hydrothermal conditions. Different NaM₂(H₃O₂)(MoO₄)₂ and M₂MoO₄(OH)₂ compositions (M = Ni, Zn) were prepared at mild temperatures (110–250 °C) for times ranging from 10 min to 24 h. Sodiated compounds were obtained after a microwave-assisted hydrothermal process at 150 °C (10–120 min) for zinc-based materials. Besides, conventional heating destabilized the sodiated NaZn₂(H₃O₂)(MoO₄)₂ phase at 110 °C, thus increasing the amount of Zn₂MoO₄(OH)₂ at temperatures up to 250 °C. NaNi₂(H₃O₂)(MoO₄)₂ phases were noted only for 10 min under microwave irradiation, while longer times promoted a chemical reaction towards a new desodiated phase. This novel Ni₂MoO₄(OH)₂ phase was also obtained by conventional hydrothermal processing (110–250 °C, 24 h). Slow precipitation rates yielded a hydrated nickel molybdate (triclinic, P) after coprecipitation followed or not by microwave irradiation. Raman spectroscopy analysis results showed a good agreement with experimental results and group-theory calculations for both sodiated and desodiated materials. A temperature-induced polymorphic transformation was observed from NiMoO₄·xH₂O (triclinic, P) to α-NiMoO₄ (monoclinic, C2/m). For all the obtained polymorphs, the relevant Raman modes were depicted, allowing us to determine their spectroscopic fingerprints. The results constitute an important basis on the understanding of the synthesis of (de)sodiated transition-metal hydroxy molybdates under hydrothermal conditions.