Epidemiological data suggest that consumption of coffee and tea is associated with a reduced risk of several chronic and degenerative diseases including cardiovascular disorders, diabetes, obesity and neurodegenerative disorders. Both coffee and tea are a rich source of phenolic compounds including chlorogenic acids in coffee; and flavan-3-ols as well as complex theaflavins and thearubigens in tea. Coffee and tea are two of the most commonly consumed beverages in the world and thus represent a significant opportunity to positively affect disease risk and outcomes globally. Central to this opportunity is a need to better understand factors that may affect the bioavailability of specific phenolic components from coffee and tea based beverages. An overview of the phenolic composition of coffee and tea is discussed in the context of how processing and composition might influence phenolic profiles and bioavailability of individual phenolic components. Specifically, the impact of beverage formulation, the extent and type of processing and the influence of digestion on stability, bioavailability and metabolism of bioactive phenolics from tea and coffee are discussed. The impact of co-formulation with ascorbic acid and other phytochemicals are discussed as strategies to improve absorption of these health promoting phytochemicals. A better understanding of how the beverage composition impacts phenolic profiles and their bioavailability is critical to development of beverage products designed to deliver specific health benefits.