In this study, we investigated the effects of germination on the secondary metabolite composition in spelt grains. Germination significantly increased the content of various metabolites in free and bound forms. Benzoxazinoids were the most important compounds in the free fraction of the 96 h germinated grains (MBOA content as the predominant compound was 277.61 ± 15.29 µg/g DW). The majority of phenolic acids were present in the bound fraction, withtrans-ferulic acid as the main component, reaching 753.27 ± 95.87 µg/g DW. The often neglectedcis-isomers of phenolic acids accounted for about 20% of the total phenolic acids. High levels of apigenin di-C-glycosides were found in spelt grains, and the schaftoside content was most affected by germination, increasing threefold. The accumulation of secondary metabolites significantly increased the antioxidant activity of germinated spelt. According to the results of this study, the content of most bioactive compounds was highest in spelt grains after 96 h of germination. These data suggest that germinated spelt could potentially be valuable for the production of functional foods.