The effects of wet chemical processing employed in device fabrication standards are studied on molybdenum oxide (MoOx) ultra-thin films. We have combined x-ray photoelectron spectroscopy (XPS), angle resolved XPS and x-ray reflectivity to gain insight into the changes in composition, structure and electronic states upon treatment of films with different initial stoichiometry prepared by reactive sputtering. Our results show significant reduction effects associated with the development of gap states in MoOx, as well as changes in the composition and structure of the films, systematically correlated with the initial oxidation state of Mo.