Bimetallic platinum–ruthenium nanoparticles stabilised by pyridine- and monophosphine-based ligands were prepared either in supercritical CO2 or in THF. TEM analyses evidenced a tendency of the nanoparticles prepared in supercritical CO2 to agglomerate. Both types of bimetallic nanoparticles were further confined into functionalised multiwalled carbon nanotubes. Upon confinement, PtRu nanoparticles stabilised by phosphine ligands appeared more agglomerated than those stabilised by the pyridine ligand. These materials were applied to cinnamaldehyde hydrogenation. Confined PtRu nanoparticles showed higher catalytic activity and selectivity than unsupported nanoparticles.