Pine seed shells and yerba mate are common wastes leftover from the food and beverage industry. This study presents the development of rigid polyurethane foams (RPUFs) filled with pine seed shells and yerba mate at 5, 10 and 15 wt%. The fillers were characterized for chemical properties using bench chemistry analyses, and the RPUFs were investigated in terms of chemical, morphological, mechanical, thermal and colorimetric characteristics. The main results indicated that yerba mate showed good compatibility with the polyurethane system, probably because its available hydroxyl groups reacted with isocyanate groups to form urethane bonds, producing increases in mechanical and thermal properties. However, pine seed shell did not appear to be compatible. Anisotropy increased slightly, as there was an increase in the percentage of reinforcement. The mechanical properties of the yerba mate reinforced foams proved stable, while there was a loss of overall up to ~50% for all mechanical properties in those reinforced with pine seed shell. Thermal properties were improved up to ~40% for the yerba mate reinforced foams, while those reinforced with pine nuts were stable. It was possible to observe a decrease in the glass transition temperature (Tg) of ~−5 °C for the yerba mate reinforced foams and ~−14 °C for the pine seed shell reinforced ones.