To preserve the sustainability of Quercus robur forests, which is at risk due to the disturbed natural regeneration, human assisted sowing of acorns or planting of oak seedlings is often performed. However, the success of these methods depends greatly on the use of high-quality sowing and planting material. Thermotherapy is thus often employed to decrease the acorn mycobiota and maintain their quality during the storage. The aim of this study was to test the impact of acorn thermotherapy, followed by a short-term storage at −1 °C or 3 °C, on the quality of related oak seedlings, which was assessed based on the easily observable morphological characteristics. Height, root collar diameter and seedling form were measured or noted for the 1284 and 1190 seedlings at the age of four months and three years, respectively. It was found that acorn thermotherapy affirmatively affected seedling height, especially at the early growth stage. Positive impact on other seedling attributes could not be decisively confirmed because of the lack of the continuity of the effect (not visible in both younger and older seedlings) and the prevailing impact of other factors. Different acorn thermotherapy conditions (temperature and duration) and short-term storage temperatures appeared to be associated only with the occurrence of stem forking at the earlier stage of seedling growth.