A comparative study was carried out on the chemical, structural and thermal properties of candelilla wax from four wax-producing communities in Mexico, which was obtained by two extraction processes, the conventional one using sulfuric acid (SA) and an eco-friendly alternative process using citric acid (CA) as the extracting agent. The waxes were analyzed by basic chemistry (acidity, saponification, ester indexes, and others), color, Fourier transform infrared spectroscopy (FTIR), Raman micro-spectroscopy, X-ray diffraction (XRD), differential scanning calorimetry (DSC), and hardness and brittleness measurements. The waxes obtained by the environmentally friendly process showed differences in their physicochemical properties when compared to waxes from the conventional process. In addition, they showed some improvements, such as lighter shades and harder waxes, suggesting that the new environmentally friendly process is a viable option.