The effect of several parameters that include carbon nanotube (CNT) pretreatment and diameter, and the nature of the metal (Co, Ru, Pd), the metal precursor (nitrate, chloride, organometallic complexes), and the solvent on the filling yield of metallic nanoparticles in CNT channels is reported. The obtained results show that it is possible to modulate the filling yield between 10 and 80 % by controlling the CNT opening and playing on the molecular recognition of the inner/outer surfaces by the metal molecular precursor. Interestingly, the best filling yields have been obtained on nitric acid oxidized nanotubes; a treatment often used for the preparation of most CNT-supported metal catalysts. The confined nanoparticles systematically show a smaller particle size than those supported on the external surface. All the prepared samples were tested for the selective hydrogenation of cinnamaldehyde, and clear correlations were established between the catalytic performances and the filling yields.