Wood coatings prolong the service life of wood-based products, but they are usually of synthetic origin. The aim of the present article is to reduce the fossil-based compounds in a commercial waterborne acrylic coating by CNC addition and to test its performance. The coatings were applied on European beech and Norway spruce wood in order to test durability against Gloeophyllum trabeum (brown wood rot) and Trametes versicolor (white wood rot). Artificial weathering and blue stain, contact angle, physical tests (adhesion, impact and scratch test), chemical (FTIR) and morpho-anatomical analysis (SEM) were carried out. CNC addition increased viscosity, limiting the spreading of the coating into wood pores as visible after SEM observation, which reduced coating adhesion on the substrate. CNC improved fungal resistance as seen by a reduced mass loss and FTIR spectroscopy thanks to crosslinks formation, which reduced water sorption as well. Color change was not significant, and, on the other hand, glossiness was reduced but resulted as more homogeneous than control. CNC addition gave good results also in blue stain protection. CNC improved scratch resistance, but no visible change to impact was registered. CNC has promising results in coatings depending on wood and fungal species and presence of further commercial additives (biocides).