In order to fully exploit the nutrient density concept, thorough understanding of the biological activity of single nutrients in their interaction with other nutrients and food components from whole foods is important. This review provides a narrative overview of recent insights into nutrient bioavailability from complex foods in humans, highlighting synergistic and antagonistic processes among food components for two different food groups, i.e., dairy, and vegetables and fruits. For dairy, bioavailability of vitamins A, B2, B12 and K, calcium, phosphorous, magnesium, zinc and iodine are discussed, whereas bioavailability of pro-vitamin A, folate, vitamin C and K, potassium, calcium, magnesium and iron are discussed for vegetables and fruits. Although the bioavailability of some nutrients is fairly well-understood, for other nutrients the scientific understanding of uptake, absorption, and bioavailability in humans is still at a nascent stage. Understanding the absorption and bioavailability of nutrients from whole foods in interaction with food components that influence these processes will help to come to individual diet scores that better reflect absorbable nutrient intake in epidemiologic studies that relate dietary intake to health outcomes. Moreover, such knowledge may help in the design of foods, meals, and diets that aid in the supply of bioavailable nutrients to specific target groups.