Diabetes mellitus is a chronic metabolic disease characterized by an imbalance in glucose homeostasis, which raises blood glucose levels. α-glucosidase enzyme hydrolyzes polysaccharides to produce glucose and since glucose is one of the primary energy sources in eukaryotes, α-glucosidase is a target for postprandial hyperglycemia regulation. The design and synthesis of new oxadiazole coumarin (5a,b and 6a,b), acryloyl chromone (10a-c) and pyrazolyl chromone (11a-c) derivatives as naturally based scaffolds are presented in this work. The new compounds were assessed as antidiabetic agents targeting α-glucosidase enzyme. With an IC50 value of 119.7 ± 4.3 μM, compound 11c demonstrated the most promising α-glucosidase inhibitory activity, superior to the standard drug acarbose (IC50 = 300.9 ± 10.9 μM). Furthermore, compared to the group of diabetic rats, the in vivo investigations demonstrated that medium and high dosages of 11c ameliorated the expression of diabetic related genes (GCK, SYT11, SNAP-25 and Ins1). According to the molecular docking results, 11c possessed the best binding energy score (-9.1 kcal/mol) within the α-glucosidase active site, outperforming the rest of the derivatives and the reference inhibitor acarbose (-8.2 kcal/mol). Lastly, an in silico molecular dynamic simulation and a pharmacokinetic study were performed on compound 11c.