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Proton exchange membrane water electrolysis (PEMWE) is a promising technology to produce high-purity renewable hydrogen gas. However, its operation efficiency is highly dependent on the usage of expensive noble metals as electrocatalysts. Replacing, decreasing, or simply extending the operational lifetime of these precious metals have a positive impact on the hydrogen economy. Mo-based electrocatalysts are often praised as potential materials to replace the Pt used at the cathode to catalyse the hydrogen evolution reaction (HER). Most electrocatalytic studies are performed in traditional three-electrode cells with different operational conditions than those seen in PEM systems, making it difficult to predict the expected material’s performance under industrially relevant conditions. Therefore, we investigated the viability of using three selected Mo-based nanomaterials (1T′-MoS2, Co-MoS2, and β-Mo2C) as HER electrocatalysts in PEMWE systems. We investigated the effects of replacing Pt on the catalyst loading, charge transfer resistance, kinetics, operational stability, and hydrogen production efficiency during the PEMWE operation. In addition, we developed a methodology to identify the individual contribution of the anode and cathode kinetics in a PEMWE system, allowing to detect the cause behind the performance drop when using Mo-based electrocatalysts. Our results indicate that the electrochemical performance in three-electrode cells might not strictly predict the performance that could be achieved in PEMWE cells due to differences in interfaces and porosity of the macroscopic catalyst layers. Among the catalysts studied, 1T′-MoS2 is truly an excellent candidate to replace Pt as an HER electrocatalyst due to its low overpotential, low charge transfer resistance, and excellent durability, reaching a high efficiency of ∼75% at 1 A cm-2 and 1.94 V. Our study highlights the importance of a continuous development of efficient noble-metal free HER electrocatalysts suitable for PEMWE systems.