Novel MoO2/C nano/microcomposites were prepared via a bottom-up approach by hydrothermal carbonization of a solution of glucose as a carbon precursor in the presence of polyoxometalates (POMs: phosphomolybdic acid [H3PMo12O40] and ammonium heptamolybdate tetrahydrate [(NH4)6Mo7O24]·4H2O). The structural characterization by FT-IR, XRPD, SEM and TEM analyses revealed the controlled formation of hierarchical MoO2/C composites with different morphologies: strawberry-like, based on carbon microspheres decorated with MoO2 nanoparticles; MoO2/C core–shell composites; and irregular aggregates in combination with ring-like microstructures bearing amorphous Mo species. These composites can be fine-tuned by varying reaction time, glucose/POM ratio and type of POM precursor. Subsequent transformations in the solid state through calcinations of MoO2/C core–shell composites in air lead to hollow nanostructured molybdenum trioxide microspheres together with nanorods and plate microcrystals or cauliflower-like composites (MoO2/C). In addition, the MoO2/C composite undergoes a morphology evolution to urchin-like composites when it is calcined under nitrogen atmosphere (MoO2/C–N2). The MoO2/C strawberry-like and MoO2/C–N2 composites were transformed into Mo carbide and nitride supported on carbon microspheres (Mo2C/C, MoN/C, and MoN/C–N2). These phases were tested as precursors in thiophene hydrodesulphurization (HDS) at 400 °C, observing the following trend in relation to the thiophene steady-state conversion: MoN/C–N2 > MoN/C > Mo2C/C > MoO2/C–N2 > MoO2/C. According to these conversion values, a direct correlation was observed between higher HDS activity and decreasing crystal size as estimated from the Scherrer equation. These results suggest that such composites represent interesting and promising precursors for HDS catalysts, where the activity and stability can be modified either by chemical or structural changes of the composites under different conditions.