Biological activity of new potential wood preservatives—ammonium- and triazolium-based ionic liquids—was determined employing screening agar-plate, agar-block, and perlite-block methods. Experiments were carried out on Scots pine (Pinus sylvestris L.) and beech (Fagus sylvatica L.) wood. This study examined the effect of the ionic liquid structure on anti-fungal efficacy, depth of penetration, and fixation in wood. It was stated that the fungicidal value of new ammonium compounds depended, above all, upon the cation structure; for Coniophora puteana, it ranged from 2.7 kg m−3 to 4.6 kg m−3. These compounds effectively protected Scots pine wood against the action of mold fungi. Ammonium ionic liquids with a nitrite anion were characterized by strong fungitoxic properties, stronger than ammonium nitrates. The application in the amount of 15 g m−2 caused an insignificant growth of mold fungi on the surface of Scots pine wood. For the mixture of 7.5% tebuconazole and 7.5% propiconazole dissolved in ionic liquids, the synergistic effect against mold fungi at the application of 15 g m−2 was found. Dissolving tebuconazole in didecyldimethylammonium nitrate repeatedly lowered the fungicidal value against brown-rot fungi, as well as increased penetration of the ionic liquids in wood. This was associated with reduced viscosity of this ionic liquid caused by the addition of 1,2,4-triazole derivatives. Quaternary derivatives of 1,2,4-triazoles showed very high activity against blue stain and wood-decaying fungi. Additionally, most of the test compounds were well-fixed in Scots pine wood. The spectral study in infrared confirmed that nitrite, nitrate anions, and didecyldimethylammonium cation were retained in the treated wood.