Non-targeted liquid chromatography-mass spectrometry (LC-MS) based metabolomics methods were used to determine whether bean consumption affects the profile of metabolites in serum and urine of individuals with peripheral artery disease. Urine and serum collected at baseline or after 8 weeks of consuming 1.5 or 3 cups per week of cooked mixed beans (pinto, red kidney, black and navy) or pulse-free foods, was extracted with acetonitrile and analyzed by non-targeted LC-QTOF-MS methods. Several compounds found in beans were present in the biological fluids indicating that these compounds may be useful markers of bean consumption. Bean consumption significantly (P<0.05) altered several endogenous metabolites including amino acids, glutathione, bile salts, phospholipids and products of arachidonic acid metabolism by cyclooxygenase. The decrease in the metabolites of an anti-hypertensive drug in urine after 8 weeks of bean consumption suggested the existence of potential drug-diet interactions that could affect the required dosage of certain anti-hypertensive medications.