Wood is a renewable, versatile material with multiple applications and the largest terrestrial pool of sequestered carbon. However, it is susceptible to degradation, mainly caused by wood-decaying fungi. Since several traditional wood preservatives have been banned owing to their detrimental effects on humans and the environment, extending the lifespan of wood products using new generation natural preservatives is an imperative from the perspectives of human health and environmental protection. Several natural compounds of plant and animal origin have been tested for their fungicidal properties, including essential oils, tannins, wood extractives, alkaloids, propolis or chitosan; and their enormous potential in wood protection has been shown. Although they are not free of limitations, the potential methods to overcome their drawbacks and enhance their bioactivity already exist, such as co-impregnation with different polymers, cross-linkers, metal chelators or antioxidants. The presence of the discrepancies between laboratory tests and the field performance, as well as legislation-related problems resulting from the lack of standards defining the quality and performance of natural protective formulations, however, create an urgent need for further thorough research and arrangements. The collaboration with other industries interested in the utilisation of natural active compounds will reduce the associated costs, thus, will facilitate the successful implementation of alternative antifungal agents.