Abstract Information regarding the use of functional foods and nutraceuticals (FFN) in combating disease is rarely communicated to health care practitioners as medicinal strategies for patients. Metabolic syndrome (MetS) is an ideal paradigm for demonstrating the therapeutic properties of FFN. Encompassing multiple etiologies, including atherogenic dyslipidemia, insulin resistance, and hypertension, MetS affects over a third of American adults. However, as disease-related risk factors accumulate over time, guidelines for treating disorders of MetS progressively de-emphasize the use of FFN. Using marine omega-3 fatty acids, plant sterols, fiber, and tomato extract as examples, the purpose of this review is to endorse FFN as long-term adjunctive therapies to pharmaceutical treatment for disorders and risk factors for MetS. An additional goal is to compare physiological and molecular targets of FFN against corresponding prescription medications. Results reveal that FFN are viable treatment strategies for disorders of MetS, complementing pharmacological interventions by targeting and improving the biological processes that foster the development of disease. Thus, efficacious FFN therapies should be emphasized throughout all stages of treatment as adjuncts to pharmacotherapy for disorders of MetS. Accordingly, new developments in FFN research must be implemented into clinical guidelines with the prospect of improving disease prognoses as accessories to prescription medications.