In this study, we report, for the first time, the synthesis of two original nanosystems, based on gold Au(III) and copper Cu(II): simple gold-copper nanoparticles (Cu0AuNPs) and enriched monopicolinate cyclam (L1)-Cu(II)-Au(III)-complex (L1@Cu2+AuNPs). The two nanomaterials differ substantially by the chelation or not of the Cu(II) ions during the NPs synthesis process. The two hybrid nanoparticles (Cu0AuNPs; L1@Cu2+AuNPs) were deeply studied from the chemical and physical point of view, using many different analytical techniques such as Raman and UV-vis spectroscopy, electron transmission microscopy, and dynamic light scattering. Both nanosystems show morphological and good chemical stability at pH 4 values and in physiological conditions during 98 h. Undifferentiated and neural differentiated murine embryonic stem cells were used as a model system for in vitro experiments to reveal the effects of NPs on these cells. The comparative study between Cu0AuNPs and L1@Cu2+AuNPs highlights that copper chelated in its +2 oxidation state in the NPs is more functional for biological application.