Burdock seeds (Fructus arctii) are used as a traditional medicine for cough, inflammation, detoxification, cancer and diabetes, usually as decoction obtained with seeds subjected to thermal pre-treatment. The present work aimed to perform the phytochemical characterization of the stir-baked and non-baked seeds of various Arctium lappa populations from nine localities. Arctiin was dominant compound in non-baked seeds ranging from 40.6–92.6 mg/g. Thermal treatment resulted in a significant transformation of phenolic compounds and arctigenin was prevalent in the baked samples with the content from 25.2–57.4 mg/g. The antidiabetic potential of baked and non-baked burdock seed extracts was further evaluated in vitro by inhibition of α-amylase and α-glucosidase activity, while molecular docking analysis was used to reveal the main molecular interactions underlying the inhibitory effects on these enzymes. In vitro study showed that stir-baked burdock seed extracts were stronger inhibitors of both enzymes compared to non-baked. The several extracts showed strong inhibition of both enzymes by almost or more than 60%, which was lower compared to acarbose (82.99% at a concentration of 1 mg/mL). Arctin and arctigenin were individually significantly stronger inhibitors of α-amylase and particularly α-glucosidase compared to burdock extracts and acarbose, and their activity was concentration dependent. Moreover, antidiabetic activity for the most active sample was determined in vivo using animals on high-fat and sucrose diet, where promising results were obtained. Briefly, after three months of administration of the stir-baked seed extract (100 mg/kg body weight), complete recovery from a hyperglycemic state was achieved. According to the obtained results A. lappa stir-baked seed extract is a potential drug with hypoglycemic action as indicated by in vitro, in vivo and in silico studies.