High pressure processing (HPP) has varying effects on bioactive compounds in food matrices. Pressure treatment at moderate temperatures can retain bioactivity and other food quality attributes of flavor, color and nutritional properties due to its minimal effects on covalent bonds of bioactive compounds. Pressure treatment at elevated temperatures, however, has been shown to induce biochemical reactions that could reduce the nutritional value of food products. The following chapter discusses effects of HPP on stability of different bioactive compounds in model systems and food matrices. As a direct consequence of the stability/instability of these bioactive compounds during HPP, their bioactivity (e.g., antioxidant capacity, bioavailability, antimutagenicity) and sensorial properties of food products are affected. Additionally, degradation mechanisms/pathways of some of these bioactive compounds are discussed in this chapter.