The long term change of the CuInSe2 surface composition under low energy hydrogen ion beam implantation at an increased substrate temperature was studied with in situ X-ray photoelectron spectroscopy (XPS). A removal of surface oxides as well as of surface contaminations due to the treatment could be observed. After storage in air, no reformation of oxides, such as SeO2 and In2O3, was detected. Ion beam hydrogenation causes considerable post-growth changes in the defect population. Initially in p-type CuInSe2, the distance between the valence band maximum (VBM) and the Fermi level increased. A reactivation of oxygen-passivated V-Se, the production of additional selenium vacancies as well as changes in the active V-Cu population, might explain these observations. At elevated substrate temperatures, the hydrogen ion beam produces an In-rich surface near to Cu2In4Se7 with a slightly reduced Se-content, independent of the initial surface composition.