Fullerene-like (FL) carbon nitride (CNx) films were deposited on Si (100) substrates by dc reactive, unbalanced, magnetron sputtering in a N2/Ar mixture from a high-purity pyrolythic graphite cathode in a dual-magnetron system with coupled magnetic fields. The N2 fraction in the discharge gas (0%–100%) and substrate bias (−25 V; −40 V) was varied, while the total pressure (0.4 Pa) and substrate temperature (450 °C) was kept constant. The coupled configuration of the magnetrons resulted in a reduced ion flux density, leading to a much lower average energy per incorporated particle, due to a less focused plasma as compared to a single magnetron. This enabled the evolution of a pronounced FL microstructure. The nitrogen concentration in the films saturated rapidly at 14–18 at. %, as determined by elastic recoil analysis, with a minor dependence on the discharge conditions. No correlations were detected between the photoelectron N1s core level spectra and the different microstructures, as observed by high-resolution electron microscopy. A variety of distinct FL structures were obtained, ranging from structures with elongated and aligned nitrogen-containing graphitic sheets to disordered structures, however, not exclusively linked to the total N concentration in the films. The microstructure evolution has rather to be seen as in equilibrium between the two competing processes of adsorption and desorption of nitrogen-containing species at the substrate. This balance is shifted by the energy and number of arriving species as well as by the substrate temperature. The most exceptional structure, for lower N2 fractions, consists of well-aligned, multi-layered circular features (nano-onions) with an inner diameter of approximately 0.7 nm and successive shells at a distance of ∼0.35 nm up to a diameter of 5 nm. It is shown that the intrinsic stress formation is closely linked with the evolution and accommodation of the heavily bent fullerene-like sheets. The FL CNx structures define the mechanical response of the films as revealed by nano-indentation. The material is highly elastic and fracture tough, and has reasonable hardness and elastic modulus values. On a nano-structured level, it is inferred the CNx stores deformation energy elastically by compression of the interplanar lattice spacing and buckling of the sheets, while crosslinks between sheets prevent gliding. Increasing the bias voltage from −25 to −40 V multiplies hardness and modulus values, while keeping their high ratio of up to 0.2, due to a higher degree of cross-linking.