We describe the electrochemical deposition of molybdenum oxide thin films prepared from aqueous solutions containing peroxo-poly and oxometallate complexes of molybdenum(VI). Electrochemical quartz crystal microgravimetry (EQCM) was used to establish corresponding reaction mechanisms for films grown at different deposition potentials. Electrodeposition from acidified sodium molybdate solutions proceeds by the reduction of molybdic acid; whilst deposition from aqueous peroxo-based solutions involves the graded reduction of several solution components, primarily comprising molybdic acid and peroxopolymolybdates. Films grown from acidified sodium molybdate solutions are weakly adherent and easily rinsed off, while those grown from peroxo-polymolybdate solutions are strongly attached and stable. Careful regulation of the deposition potential allows for controlled growth of distinct molybdenum oxide compositions to produce films with varied water content and valency. Electrochemical deposition through sacrificial colloidal-crystal templates is also demonstrated to prepare macroporous thin films comprising hexagonally close-packed arrays of spherical pores.