In this study, olive pit powders were added to a polyurethane-acrylate paint for examining the impact of two alternative functionalization processes in increasing the filler hydrophobicity in an effort to increase the durability of the paint. In order to look into potential changes in morphology and appearance owing to the surface conversion treatments of the two bio-based additives, the coatings were examined using electron microscopy and colorimetric tests. The coating’s resilience and the hydrophobic/hydrophilic role of the fillers were evaluated by salt spray chamber exposure, contact angle measurements, paint liquid resistance, UV-B exposure, and electrochemical impedance spectroscopy measurements, which highlighted the reduction in water absorption inclination of the filler made of lignocellulose due to the silane and wax functionalization. This study demonstrated that the bio-based filler, if properly functionalized, can actually be implemented as multifunctional pigment in waterborne paints, giving specific aesthetic characteristics, but also improving the barrier performance of the polymeric matrix and increasing the durability of the composite coating.