Reduced graphene oxide aerogels doped with nitrogen have been prepared via two different strategies, namely, direct doping of rGO nanosheets with NH3 (GANH3) and coating the rGO nanosheets with an N-containing amorphous carbon derived from polydopamine (GADA). Both methods lead to comparable N/C ratios (3.4–4.7 %) but the relative contribution of quaternary nitrogen is 30 % for GADA while only 15 % for GANH3. Moreover, the N is incorporated within graphene lattice for GANH3 while it is within an amorphous carbon layer on top of graphene nanosheets for GADA. The Ru catalyst supported on the aerogels exhibited very distinct performance in the selective oxidation of benzyl alcohol depending on the support material despite having similar Ru particle size. The best performance for 5 wt% Ru on GADA can be explained by the larger reduction extent of Ru and the more hydrophobic surface. The open macroporosity of the aerogel makes it an excellent platform for using as structured catalyst in a continuous flow process.