► Control of the reduction parameters on chemical reductions of graphene oxide (GO) leads to different deoxygenation degrees. ► Reduction proceeds by elimination of the most labile functional groups, mostly located on basal plane positions. ► GO sheets are composed of intermingled oxidized and non-oxidized regions, whose relative area depends on the reduction degree. Chemical reduction of exfoliated graphite oxide (graphene oxide) has become one of the most promising routes for the mass production of graphene sheets. Nonetheless, the material obtained by this method exhibits considerable structural disorder and residual oxygen groups, and reports on their microscopic structure are quite scarce. We have investigated the structure and chemistry of graphene oxide samples reduced to different degrees using atomic force and scanning tunneling microscopy (AFM/STM) as well as X-ray photoelectron spectroscopy (XPS) and temperature-programmed desorption (TPD), respectively. TPD and XPS results indicate that reduction proceeds mainly by eliminating the most labile oxygen groups, which are ascribed to epoxides and hydroxyls on basal positions of the graphene plane. AFM/STM shows that the sheets are composed of buckled oxidized regions intermingled with flatter, non-oxidized ones, with the relative area of the latter increasing with the reduction degree.