This paper presents possibilities for increasing the decay and mould resistance of Scots pine (Pinus sylvestris L.) sapwood by treatment: (1) in one step with mixtures of aqueous solutions of methyltrimethoxysilane (0, 5, 10, 20 or 30 % MTMS) and benzalkoniumchloride (0, 0.5, 1, 2 or 3 % BAC), and (2) in two steps, first with BAC and then with MTMS. Prior to fungal resistance tests, the treated and reference specimens were not or were subjected to artificial ageing in distilled water and in Xenotest, respectively. Insufficient anti-decay efficiency of MTMS against the brown-rot fungus Coniophora puteana and the white-rot fungus Trametes versicolor was improved in the presence of BAC, usually more apparent if this fungicide was used first and in higher concentrations. After both artificial ageing modes, the decay resistance of treated pine specimens decreased approximately 1.2–1.8 times. The none anti-mould efficiency of MTMS improved in the presence of BAC—significantly against the mould Penicillium brevicompactum but only minimally against the mould Aspergillus niger.