The main goal of the investigation was to measure and estimate the thermal stability of pinosylvin, pinosylvin monomethyl ether, robinetin, and dihydrorobinetin, i.e., characteristic compounds of wood of Scots pine and black locust, respectively. The pure compounds were analyzed with chromatography before and after they were steam-sterilized and oven-dried. Detailed thermogravimetric analysis was followed to check the thermal decomposition of the stilbenes and flavonoids of wood. The tested phenolic compounds were susceptible to thermal degradation. After the steam-sterilization and oven drying, the amount of investigated phenolic extractives decreased by more than a half. The thermogravimetric analysis showed that stilbenes decompose differently than flavonoids, which can be attributed to the different chemical structures. Twenty minutes of steam sterilization followed by 24 h of oven drying decreased the amount of phenolic compounds in the vials; however, after the applied thermal treatments, the stilbenes and robinetins stayed available in such quantities that they can still provide sufficient bioactivity.