A comprehensive experimental and theoretical study of the surface chemistry of ruthenium nanoparticles supported on/in multi-walled carbon nanotubes (CNTs) is reported that could pave the way to the rational design of metal–carbon nanocomposites. It is shown that the oxidation of CNTs by nitric acid that creates various oxygen surface functional groups (SFGs) on the CNT external surface is a crucial step for metal grafting. In particular, it is demonstrated that carboxylic acid, carboxylic anhydride, and lactone groups act as anchoring centers for the Ru precursor, presumably as surface acetato ligands. The HNO3 treatment that also allows CNT opening contributes to the endohedral Ru deposition. The stability of Ru nanoparticles, modeled by a Ru13 cluster, on different adsorption sites follows the order: Gr-DV-(COOH)2 > Gr-DV > Gr (where DV is a double vacancy and Gr the graphene surface). It is evidenced that, after a high-temperature treatment performed in order to remove the SFGs, the Ru/CNT material can react with oxygen from air via a surface reconstruction reaction, which reforms a stable Ru-acetato interface. The mechanism of this reaction has been investigated by DFT. These Ru/CNT catalysts are extremely stable, keeping a mean particle size <2 nm, even after heating at 973 K under a hydrogen atmosphere.