There has been a sharp rise in the global prevalence of diabetes, obesity, and their comorbid conditions within the last decade prompting significant research into possible causes and cure via therapeutic intervention and lifestyle adjustments. Here, the molecular bases of antidiabetic plants used in the prehistorical treatment of diabetes and obesity are reviewed with particular focus on saponin as the phytotherapeutic principle. Until recently, the phytotherapeutic potentials of saponins have been masked in the heterogeneity of phytochemicals co-extractable during traditional preparations. With improved technique of purification and cutting edge biological assay methods, saponins have emerged as a regulator of primary biofuel availability through direct interaction with energy metabolism, cell signaling, and gene expression. Specific cases of lipoprotein lipase/peroxisome proliferator-activated receptor (PPAR)-gamma/phosphatidylinositide 3-kinase (PI-3-K)/protein kinase B (Akt) activation, adiponectin gene upregulation, fatty acid binding protein 4 repression (FABP4), and glucose transporter type 4 (Glut4) membrane exocytosis have been documented which provide molecular basis for hypocholesterolemic, hypoglycemic, and anti-obesity manifestations observed in experimental animals following saponin treatment. Although intensified research is required to characterize the pharmacophoric features in saponins exhibiting these interactions, however, this preliminary lead is valuable if the world will be free of diabetes, obesity, hypertension, hyperlipidemia, and atherosclerosis in no distant future.