Tannins and their toxic effects against various decay organisms have been interrelated for centuries. As natural products have gained more interest, waste from several production fields abundant in tannins has yielded promising components for wood preservation. In this work, the main approach was to split condensed tannins into smaller fractions by chemical hydrolysis and evaluate their suitability for beech wood impregnation. Commercial extract from black wattle was treated with mineral acid of low concentration. The volatile hydrochloric acid was completely removed after reaction by evaporation in the course of freeze-drying. The modified extract was then applied as aqueous solution into beech wood. The water resistance of the modified beech wood was not increased significantly, and scanning electron microscopy (SEM) showed no evidence of tannin successful bonding within wood cells. Nevertheless, after strong leaching cycles, part of the extract accumulated in fibers. Moreover, lyophilization was found to be a suitable technique to eliminate volatile acids from temperature-sensitive extracts, such as tannins. These findings could help in the development of water-borne tannin formulations for wood protection, while using phlobaphene formation as a potential natural pathway of tannin autocondensation.