Phytochemicals are increasingly studied for their potential to inhibit HMG-CoA reductase (HMGR) and alpha-amylase enzymes, which are key targets in managing hypercholesterolemia and diabetes. The inhibition of HMGR reduces cholesterol synthesis, while alpha-amylase inhibition helps control postprandial blood glucose levels. This study used computational techniques, including molecular docking and ADMET (Absorption, Distribution, Metabolism, Excretion, and Toxicity) predictions, to evaluate the potential of five Ginkgo biloba biflavonoids—amentoflavone, bilobetin, ginkgetin, isoginkgetin, and sciadopitysin—as dual inhibitors of these enzymes. The molecular docking results demonstrated that amentoflavone (-10.1 kcal/mol) and bilobetin (-9.8 kcal/mol) exhibited stronger binding affinities to HMGR than the reference drug atorvastatin (-9.3 kcal/mol). Similarly, for α-amylase, amentoflavone (-11.5 kcal/mol), bilobetin (-11.3 kcal/mol), and ginkgetin (-11.1 kcal/mol) surpassed the binding affinity of the reference drug acarbose (-10.5 kcal/mol). These consistently strong binding affinities indicate that both amentoflavone and bilobetin have the potential to act as dual inhibitors of these two enzymes. Our ADMET analysis revealed that bilobetin demonstrated favorable drug-like properties, adhering to Lipinski’s rule of five, which predicts good oral bioavailability. Although bilobetin exhibited low gastrointestinal absorption, it was predicted to be non-mutagenic and non-hepatotoxic and demonstrated no significant toxicity risks, making it a highly promising candidate for further drug development. These important findings underscore the potential of Ginkgo biloba biflavonoids for addressing metabolic disorders. Future in vitro and in vivo studies are essential to validate these in silico results, providing deeper insights into their therapeutic applications and contributing to the development of novel dual-action drugs targeting hypercholesterolemia and diabetes.