For an optimal use of copper nanoparticles in catalysis, in-depth understanding of the reaction mechanisms and fine characterization of final products are equally relevant. Indeed, both have a direct impact on the nanoparticles core and surface. So far, most insights are coming from characterization techniques focusing on the inorganic component, e.g. the nanoparticle core. Molecular techniques are often overlooked. This results in an incomplete description of the organic shell of ligands and of the molecular process governing the inorganic core nature. This is detrimental to finely interpret the nanoparticles behavior in catalytic processes. In this study, we showed that the copper precursor has a strong influence on the inorganic component of the nanoparticles. This was studied by thorough characterization of the organic reactions happening during the synthesis, quantitatively by 1H Nuclear Magnetic Resonance and qualitatively by infra-red spectroscopy and electrospray ionisation-mass spectrometry. The reduction of Cu(OAc)2 by oleylamine resulted in high amount of water and few byproducts while the reduction of Cu(acac)2 resulted in low amount of water and many products. The resulting nanoparticles showed a different ability to further dehydrogenate and transaminate oleylamine in the synthesis reaction pot. This was explained by the presence of a copper oxide phase in the nanoparticles from Cu(OAc)2. This study underlines the relevance of examining side-reaction of the organic species involved in nanoparticles synthesis to design nanoparticles with controlled features and catalytic properties.