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The European beech (Fagus sylvatica L.) is the most grown broadleaved tree species in Czech forests. Annual demand for beechnuts is 56 tons in the Czech Republic. The dormancy can vary greatly from year to year, among seed lots, and among seeds within a seed lot. Beechnuts are typical examples of seeds with a variable or often deep dormancy. In the standard method the dormancy breaking treatment is applied after storage and just before sowing (dormant beechnuts). A new method is the application of the dormancy breaking treatment immediately after seed collection, followed by drying of the pre-treated seeds and their storage (non-dormant beechnuts). This study aims to optimize stratification period by pre-chilling seeds for different durations, and follows changes in the germination ability and emergence rate of dormant and non-dormant beechnuts during 2–3 years of storage. After being collected, the beechnuts were stratified without medium for 9, 11, 13 and 15 weeks, then dried down to 10% and stored as non-dormant seeds. The other part of beechnuts was dried down to 10% after seed collection, then stored and stratified for 10 weeks before sowing (dormant seeds). The beechnuts stored 8–20 months in dormant state had significantly higher viability and germination capacity compared to beechnuts stored 4–18 months in the non-dormant state. Viability and germination capacity significantly decreased with the prolonged stratification. Good germination capacity and emergence rate of the non-dormant beechnuts was reported after stratification taking 9–11 weeks. After two years the stored dormant beechnuts emerged in greenhouse more (43–68%) than stored non-dormant ones (22–69%). In field beds the average emergence rate of stored non-dormant beechnuts of all three seed lots dropped to 13–45%. The beechnuts with deeper dormancy respond to stratification and drying after seed collection by slight reduction of viability, germination capacity and emergence rate.