This research discusses the CO2 valorization via hydrogenation over the non-noble metal clusters of Ni and Cu supported on graphitic carbon nitride (g-C3N4). The Ni and Cu catalysts were characterized by conventional techniques including XRD, AFM, ATR, Raman imaging, and TPR and were tested via the hydrogenation of CO2 at 1 bar. The transition-metal-based catalyst designed with atom-economy principles presents stable activity and good conversions for the studied processes. At 1 bar, the rise in operating temperature during CO2 hydrogenation increases the CO2 conversion and the selectivity for CO and decreases the selectivity for methanol on Cu/CN catalysts. For the Ni/CN catalyst, the selectivity to light hydrocarbons, such as CH4, also increased with rising temperature. At 623 K, the conversion attained ca. 20%, with CH4 being the primary product of the reaction (CH4 yield >80%). Above 700 K, the Ni/CN activity increases, reaching almost equilibrium values, although the Ni loading in Ni/CN is lower by more than 90% compared to the reference NiREF catalyst. The presented data offer a better understanding of the effect of the transition metals’ small metal cluster and their coordination and stabilization within g-C3N4, contributing to the rational hybrid catalyst design with a less-toxic impact on the environment and health. Bare g-C3N4 is shown as a good support candidate for atom-economy-designed catalysts for hydrogenation application. In addition, cytotoxicity to the keratinocyte human HaCaT cell line revealed that low concentrations of catalysts particles (to 6.25 μg mL–1) did not cause degenerative changes.