Three commercial silicone emulsions with different functional groups i.e., quat-silicone micro-emulsion (<40 nm particle size), amino-silicone macro-emulsion (110 nm), and silicone macro-emulsion with alkyl-modified side groups (740 nm) were used to protect wood samples against fungal decay. The addition of the emulsions to an agar growth medium revealed that all three silicone formulations inhibited the growth of Coniophora puteana and Trametes versicolor compared to the controls without silicone. Wood mini-blocks of pine sapwood and beech wood were treated with 2%, 5%, 10%, and 15% concentration of silicone emulsions and tested for their resistance against basidiomycete decay. Quat-silicone and amino-silicone emulsions at higher concentrations imparted resistance of wood to both types of basidiomycetes, while the alkyl-modified silicone formulation did not enhance the resistance. In a soft rot test according to ENV 807, wood treated with an amino-sililcone emulsion showed the lowest weight loss and loss of dynamic MOE. Quat-silicone micro-emulsion had a lower effect, while the alkyl-modified silicone emulsion did not cause reduction in weight and strength loss compared to the untreated controls. The increased resistance against soft rot might be attributed to a lag in fungal colonization rather than to a sustained effect of protection.