The influence of inert gases (Ne, Ar, Kr) on the sputter process of carbon and carbon-nitride (CNx) thin films was studied using reactive high power pulsed magnetron sputtering (HiPIMS). Thin solid films were synthesized in an industrial deposition chamber from a graphite target. The peak target current during HiPIMS processing was found to decrease with increasing inert gas mass. Time averaged and time resolved ion mass spectroscopy showed that the addition of nitrogen, as reactive gas, resulted in less energetic ion species for processes employing Ne, whereas the opposite was noticed when Ar or Kr were employed as inert gas. Processes in nonreactive ambient showed generally lower total ion fluxes for the three different inert gases. As soon as N2 was introduced into the process, the deposition rates for Ne and Ar-containing processes increased significantly. The reactive Kr-process, in contrast, showed slightly lower deposition rates than the nonreactive. The resulting thin films were characterized regarding their bonding and microstructure by x-ray photoelectron spectroscopy and transmission electron microscopy. Reactively deposited CNx thin films in Ar and Kr ambient exhibited an ordering toward a fullerene-like structure, whereas carbon and CNx films deposited in Ne atmosphere were found to be amorphous. This is attributed to an elevated amount of highly energetic particles observed during ion mass spectrometry and indicated by high peak target currents in Ne-containing processes. These results are discussed with respect to the current understanding of the structural evolution of a-C and CNx thin films.