There is growing interest in the development of non-toxic, natural wood preservation agents to replace conventional chemicals. In this paper, the antifungal activities of silver nanoparticles, chitosan oligomers, and propolis ethanolic extract were evaluated against white-rot fungus Trametes versicolor (L.) Lloyd, with a view to protecting Populus spp. wood. In order to create a more realistic in-service type environment, the biocidal products were assessed according to EN:113 European standard, instead of using routine in vitro antimicrobial susceptibility testing methods. Wood blocks were impregnated with the aforementioned antifungal agents by the vacuum-pressure method in an autoclave, and their biodeterioration was monitored over 16 weeks. The results showed that treatments based on silver nanoparticles, at concentrations ranging from 5 to 20 ppm, presented high antifungal activity, protecting the wood from fungal attack over time, with weight losses in the range of 8.49% to 8.94% after 16 weeks, versus 24.79% weight loss in the control (untreated) samples. This was confirmed by SEM and optical microscopy images, which showed a noticeably higher cell wall degradation in control samples than in samples treated with silver nanoparticles. On the other hand, the efficacy of the treatments based on chitosan oligomers and propolis gradually decreased over time, which would be a limiting factor for their application as wood preservatives. The nanometal-based approach is thus posed as the preferred choice for the industrial treatment of poplar wood aimed at wood-based engineering products (plywood, laminated veneer lumber, cross-laminated timber, etc.).