Traditional wood preservatives based on biocides are effective against wood-deteriorating organisms because of their toxicity. By contrast, modified woods are non-toxic by definition. To investigate the efficiency of various wood modifications, quantitative real-time polymerase chain reaction (qPCR) was used to profile the DNA amounts of the white-rot fungus Trametes versicolor (L.) [Lloyd strain CTB 863 A] during an 8-week-long growth period in treated Pinus sylvestris (L.) sapwood. The studied wood was modified by acetylation, furfurylation, and thermal treatment. The traditional wood preservatives bis-(N-cyclohexyldiazeniumdioxy)-copper (Cu-HDO) and chromated copper arsenate (CCA) were used as references, whereas untreated P. sylvestris (L.) sapwood served as a control. The maximum levels of fungal DNA in native wood occurred at the end of the experiment. For all wood treatments, the maximum fungal DNA level was recorded after an incubation period of 2 weeks, followed by a decline until the end of the trial. For the preservative-treated woods, Cu-HDO showed the lowest level of fungal DNA throughout the experiment, indicating that exploratory hyphal growth is limited owing to the phytotoxicity of the treatment. The other treatments did not inhibit the exploratory hyphal growth phase. We conclude that qPCR studies of hyphal growth patterns within wood should provide a powerful tool for evaluating and further optimizing new wood protection systems.