Electrocatalytic hydrogenation (ECH) of organics of biomass origin represents a promising strategy to enable integration of renewables and circular economy practices. However, most electrocatalysts investigated for ECH remain largely based on precious metals. Nanostructured materials based on transition metals encapsulated in a nitrogenated carbon matrix (M@C:N) offer a promising alternative. Herein, we report on the synthesis of Mo@C:N and W@C:N composites that display the same metal atomic concentrations and thus allow for a comparative study of the effect of the metal center identity on the properties of such heterostructured materials and their performance in the ECH of benzaldehyde, a diagnostic organic substrate. A combination of structural characterization methods indicates that the type of metal impacts carbon porosity and metal surface concentration in the synthesized structures. W displays a higher tendency to yield encapsulated nanoparticles compared to Mo, which is instead present with surface excess but at predominantly high oxidation states. Electrolysis studies at varying potentials demonstrate high product rates of benzaldehyde hydrogenation, with good selectivity for the production of the corresponding alcohol vs the dimerization side product. Turnover frequency (TOF) estimates under the operational conditions tested suggest that replacing Mo-centers with W-centers in M@C:N architectures improves overall performance. A comparison of performance indicators with those for Pt-group metals suggests that W@C:N could be a competitive material for practical implementations of ECH.