Natural filler-based composites are an environmentally friendly and potentially sustainable alternative to synthetic or plastic counterparts. Recycling polymers and using agro-industrial wastes are measures that help to achieve a circular economy. Thus, this work presents the development and characterization of a 3D printing filament based on recycled polypropylene and cocoa bean shells, which has not been explored yet. The obtained composites were thermally and physically characterized. In addition, the warping effect, mechanical, and morphological analyses were performed on 3D printed specimens. Thermal analysis exhibited decreased thermal stability when cacao bean shell (CBS) particles were added due to their lignocellulosic content. A reduction in both melting enthalpy and crystallinity percentage was identified. This is caused by the increase in the amorphous structures present in the hemicellulose and lignin of the CBS. Mechanical tests showed high dependence of the mechanical properties on the 3D printing raster angle. Tensile strength increased when a raster angle of 0° was used, compared to specimens printed at 90°, due to the load direction. Tensile strength and fracture strain were improved with CBS addition in specimens printed at 90°, and better bonding between adjacent layers was achieved. Electron microscope images identified particle fracture, filler-matrix debonding, and matrix breakage as the central failure mechanisms. These failure mechanisms are attributed to the poor interfacial bonding between the CBS particles and the matrix, which reduced the tensile properties of specimens printed at 0°. On the other hand, the printing process showed that cocoa bean shell particles reduced by 67% the characteristic warping effect of recycled polypropylene during 3D printing, which is advantageous for 3D printing applications of the rPP. Thereby, potential sustainable natural filler composite filaments for 3D printing applications with low density and low cost can be developed, adding value to agro-industrial and plastic wastes.