Photoactive nanoparticles are used to reduce microbial colonization and self-clean surfaces of materials such as glass and ceramics. To test whether such an approach is feasible for wood surfaces, we treated radiata pine samples with TiO2 (rutile and anatase) or ZnO nanoparticles and then coated the samples with different finishes. Coated samples and uncoated controls were exposed outdoors for six months. After exposure, fungi colonizing wood surfaces were identified using molecular techniques and microscopy, and colour changes in the wood samples were also measured. Treatment of uncoated surfaces with nanoparticles reduced the discolouration of wood during weathering but had little effect on colonization of wood by black mould fungi. In contrast, pretreatment of samples with titanium dioxide nanoparticles increased the number and diversity of fungi including basidiomycetes colonizing coated samples, whereas zinc oxide nanoparticles had the opposite effect. Zinc oxide nanoparticles, however, were less effective than rutile titanium dioxide nanoparticles at reducing the discolouration of coated samples exposed to natural weathering. We conclude that none of the photoactive nanoparticles on their own are able to reduce microbial colonization and discoloration of samples. This suggests that it may be difficult to create self-cleaning wood surfaces using photoactive nanoparticles.