We investigate the reproducibility of repeated intercalation of hydrogen in graphene/Ge (110) and the formation of H2 nanobubbles after thermal treatments. By exploiting high-resolution electron energy loss, we obtain direct spectroscopic fingerprints of H2 trapped gas in the samples when nanobubbles are present and we are able to track the effectiveness of H intercalation via the Ge–H vibrational mode. We correlate the effectiveness of interface re-hydrogenation to the presence of structural defects in graphene as highlighted by Raman spectroscopy. The π-plasmon mode of graphene on Ge (110) is investigated as a function of the hydrogen presence at the interface, revealing that, independent of the hydrogen intercalation status, graphene is weakly interacting on Ge (110).