Atomic deuterium (D) adsorption on free-standing nanoporous graphene obtained by ultra-high vacuum D2 molecular cracking reveals a homogeneous distribution all over the nanoporous graphene sample, as deduced by ultra-high vacuum Raman spectroscopy combined with core-level photoemission spectroscopy. Raman microscopy unveils the presence of bonding distortion, from the signal associated to the planar sp2 configuration of graphene toward the sp3 tetrahedral structure of graphane. The establishment of D–C sp3 hybrid bonds is also clearly determined by high-resolution X-ray photoelectron spectroscopy and spatially correlated to the Auger spectroscopy signal. This work shows that the low-energy molecular cracking of D2 in an ultra-high vacuum is an efficient strategy for obtaining high-quality semiconducting graphane with homogeneous uptake of deuterium atoms, as confirmed by this combined optical and electronic spectro-microscopy study wholly carried out in ultra-high vacuum conditions.