Hydrogenated sub-stoichiometric oxides exhibiting perovskite structure such as those of tungsten and of molybdenum( H:MOx, where M = W or Mo and x < 3) were treated by microwave (MW) post-deposition annealing in air. The purpose of this treatment was to vibrate and therefore heat, the O-H bonds present in them only, without heating the rest of the lattice and the substrate. It was shown that, contrary to thermal heating, MW annealing did not affect significantly the oxygen and hydrogen contents in samples, but it caused an atomic rearrangement; more significant for H: MoOx than for H: WOx films, attributed to the layered, two-dimensional structure of the former contrary to the three-dimensional one of the latter. It was concluded that MW annealing at appropriately chosen frequencies may potentially be used to improve atomic ordering in other materials without causing alterations of their chemical composition and avoiding the heating of the substrate. (C) 2016 Elsevier B.V. All rights reserved.