This study aimed to present the influence of bio-based and anthraquinone dyes and their combinations on the optical properties of ethylene-propylene (EPM) composites after thermo-oxidative and climatic aging. Therefore, the chosen polymer was filled with a natural, plant-origin flavonoid—quercetin, and with two commercial anthraquinone dyes (C.I. Solvent Yellow 163 and C.I. Solvent Red 207). The manufactured polymer composites were subjected to accelerated aging tests: weathering and thermo-oxidation, respectively. Examination of the materials’ properties indicated that the combination of synthetic and natural dyes can result in better resistance to oxidizing agents and higher thermal stability of ethylene-propylene products. Moreover, color change of quercetin-containing samples due to exposure to simulated atmospheric conditions could be a promising solution for use as aging indicators in intelligent packaging materials that will inform about the ongoing degradation process. Another interesting finding is that these samples exhibited good fungistatic activity against Candida albicans yeast and Aspergillus niger mold. Overall, this novel solution based on hybrid polymer composites containing natural and commercial dyes is a more environmentally friendly alternative to traditional materials used in the plastic packaging industry with better and more desirable properties.