Diabetes mellitus (DM) is a group of syndromes and complications characterized by hyperglycemia, metabolic disorders in lipids, carbohydrates, and proteins. It causes an increased risk of vascular complications. A methanolic extract of Scrophularia deserti was found to reduce blood glucose in basal conditions and after heavy glucose load in normal rats. S. deserti extract lowered the hyperglycemia in streptozotocin-induced diabetic rats (33.33 % at 200 mg/kg, 41.43 % at 400 mg/kg, 2-, and 4-hours following administration when compared to standard glibenclamide (52.05 %). Furthermore, the in vitro activity of the extract was screened against two major diabetes targets; human α-glucosidase and human α-amylase, and showed 88–87 % inhibition effect compared to reference drugs. In addition, the Scrophularia deserti extract was assayed for detection of its antioxidant assay as a free radical scavenger. In the cytotoxicity experiment, the extract exhibited a good cytotoxic selectivity to cancer over normal cell lines. Herin, we categorized all active components existing in the plant extract as defined by LC-MS tool for further computational studies. Certain molecular modeling studies have been done including docking experiments and molecular dynamic simulations for the most predicted potent active metabolites; Caffeic acid 3-glucoside and 1-O-feruloyl-β-d-glucose. The results revealed good binding and stability behavior within the active sites of both targets.