In this work, different materials for three-dimensional (3D)-printing were studied, which based on polycaprolactone with two natural additives, gum rosin, and beeswax. During the 3D-printing process, the bed and extrusion temperatures of each formulation were established. After, the obtained materials were characterized by mechanical, thermal, and structural properties. The results showed that the formulation with containing polycaprolactone with a mixture of gum rosin and beeswax as additive behaved better during the 3D-printing process. Moreover, the miscibility and compatibility between the additives and the matrix were concluded through the thermal assessment. The mechanical characterization established that the addition of the mixture of gum rosin and beeswax provides greater tensile strength than those additives separately, facilitating 3D-printing. In contrast, the addition of beeswax increased the ductility of the material, which makes the 3D-printing processing difficult. Despite the fact that both natural additives had a plasticizing effect, the formulations containing gum rosin showed greater elongation at break. Finally, Fourier-Transform Infrared Spectroscopy assessment deduced that polycaprolactone interacts with the functional groups of the additives.