Recent progress in wood preservative research has led to the use of insoluble copper carbonate in the form of nano- to micron-sized particles in combination with known triazole fungicides to combat fungal decay and thus decrease physical material properties. Evidently, particle-based agents could lead to issues regarding impregnation of a micro-structured material like wood. In this study, we analyzed these limitations via silicon dioxide particles in impregnation experiments of pine and beech wood. In our experiments, we showed that limitations already existed prior to assumed particle size thresholds of 400–600 nm. In pine wood, 70 nm sized particles were efficiently impregnated, in contrast to 170 nm particles. Further we showed that surface functionalized silica nanoparticles have a major impact on the impregnation efficiency. Silica surfaces bearing amino groups were shown to have strong interactions with the wood cell surface, whereas pentyl chains on the SiO2 surfaces tended to lower the particle–wood interaction. The acquired results illustrate an important extension of the currently limited knowledge of nanoparticles and wood impregnation and contribute to future improvements in the field of particle-based wood preservatives.