Flavonoids, one of the most abundant phytochemicals in a diet rich in fruits and vegetables, have been recognized as possessing anti-proliferative, antioxidant, anti-inflammatory, and estrogenic activities. Numerous cellular and animal-based studies show that flavonoids can function as antioxidants by preventing DNA damage and scavenging reactive oxygen radicals, inhibiting formation of DNA adducts, enhancing DNA repair, interfering with chemical damage by induction of Phase II enzymes, and modifying signaling pathways. Recent evidence also shows their ability to regulate the immune system. However, findings from clinical trials have been mixed with no clear consensus on dose, frequency, or type of flavonoids best suited to elicit many of the beneficial effects. Delivery of these bioactive compounds to their biological targets through “targeted designed” food processing strategies is critical to reach effective concentration in vivo. Thus, the identification of novel approaches that optimize flavonoid bioavailability is essential for their successful clinical application. In this review, we discuss the relevance of increasing flavonoid bioavailability, by agricultural engineering and “targeted food design” in the context of the immune system and cancer.