A combination of experimental spectroscopies (UV-vis and Fourier-transform infrared) and computational modeling was used to investigate the coordination of small ligands (aminopropanol and propanediol) to Pd species during the metal nanoparticle formation process. Differences emerged between O- (propanediol) and N-containing (aminopropanol) ligands. In particular, a strong interaction between the NH amino group and Pd2+ ions could be inferred on the basis of spectroscopic evidences, which was corroborated by theoretical simulations, which confirmed the preferential coordination of aminopropanol through the NH group. This interaction seems to potentially cause the aminopropanol ligand to control the particle shape through a selective blocking of Pd(100) facets, which promote the growth on the Pd(111) facets.