A Proton flow reactor (PFR) system stores energy in the form of hydrogen in porous carbon particles in slurry electrodes. However, the hydrogen storage mechanisms and the reactions in this system are not well understood. In this study, we design and fabricate a microfluidic proton flow reactor (MPFR) as a small-scale PFR to enable in-situ visualisation of the key processes underlying PFR operations. We observe the behaviour of slurries and water in both hydrogen and oxygen sides with emphasis on processes in the vicinity of membranes. We use fluorescence microscopy with quinine to visualize hydronium transport from the oxygen to the hydrogen side and employ in-situ Raman spectroscopy to analyze surface structural changes in carbon particles before and after charging. Fluorescence microscopy demonstrates the formation of hydronium ions on the oxygen side and their subsequent migration to the hydrogen side, proving that the oxygen evolution reaction occurs on the oxygen side. Raman heat maps prove the formation of carbon–hydrogen bonding in particles after they are charged with PFR. Although the MPFR is operated at non-optimal slurry concentrations to allow optical access, we demonstrate that it provides maximum hydrogen storage capacity of 0.64 wt%.