The European beech (Fagus sylvatica L.) wood was thermally modified in the presence of paraffin at the temperatures of 190 or 210 °C for 1, 2, 3 or 4 h. A significant increase in its resistance to the brown-rot fungus Poria placenta (by 71.4%–98.4%) and the white-rot fungus Trametes versicolor (by 50.1%–99.5%) was observed as a result of all modification modes. However, an increase in the resistance of beech wood surfaces to the mold Aspergillus niger was achieved only under more severe modification regimes taking 4 h at 190 or 210 °C. Water resistance of paraffin-thermally modified beech wood improved—soaking reduced by 30.2%–35.8% and volume swelling by 26.8%–62.9% after 336 h of exposure in water. On the contrary, its mechanical properties worsened—impact bending strength decreased by 17.8%–48.3% and Brinell hardness by 2.4%–63.9%.