Low molecular weight plant secondary metabolites are involved in the interactions between plants and their environment. Many plant secondary metabolites are involved in the plant´s defense mechanisms against biotic and abiotic stress, they attract pollinators, and various other functions are suggested. However, specific functions of many secondary metabolites in the plant are not known yet. As constituents of plant-based foods, they have many functional and potential physiological effects. Depending on the phytochemicals, they act as colorants in food products, delay lipid oxidation improving shelf-life, interact with enzymes in food products and humans, show anti-inflammatory effects in humans etc. Activity guided fractionation is as a well-known approach that can be applied to identify plant secondary metabolites with specific functions. In the past, we used this concept to identify, for example, amylase and lipase inhibiting phytochemicals. Furthermore, we are interested in the fate of specific phytochemicals during food processing operations and develop methods to identify and quantitate specific phytochemicals, their conjugates, and degradation products.