The use of supported metallic nanoparticles (NPs) is fundamental for the development of new catalysts with high activity and selectivity. For this reason, the choice of a suitable support, the selection of metal precursors and the preparation methods become quite important. In the present work, we show the structural effects induced on metal vapour synthesis (MVS) derived Cu NPs by different carbon-based supports such as poly-4-vinylpyridine (PVPy) and carbon and how these effects can affect their catalytic activities in Huisgen azide-alkyne cycloaddition reactions (CuAAC). The influence of the two supports on the structure of the Cu NPs was studied using high-resolution transmission electron microscopy (HRTEM) and X-ray absorption fine structure (XAFS) spectroscopy. As shown by XAFS analysis, Cu NPs, immobilized on PVPy, resulted in a Cu(I) oxidized phase while the ones on carbon were in a Cu(II) phase. The structural effects induced by the different supports determined a completely different catalytic behaviour of the two catalytic systems in a model CuAAC reaction: the PVPy-supported Cu system was active and re-usable whereas the analogous carbon-based system was almost inactive.