Fresh and processed food products are rich in bioactive molecules, including polysaccharides, vitamins, carotenoids, peptides, antioxidants, phenolics, phytosterols, and novel lipids. Bioactive molecules in food could prevent several diseases (i.e., metabolic syndrome, cardiovascular diseases, cancer, etc.). Thus, consumer awareness is growing about the health-promoting impact of food bioactive molecules. Health claims are essential added-value features, wherein health-enhancing potential of bioactives depend on their chemical structure. On the other hand, the investigation of the structure-function relationship of food bioactive molecules is of importance. In this regard, Molecules is delighted to highlight the importance of food bioactive molecules and their effect on health. In this Special Issue of Molecules, researchers are invited to contribute original research and up-to-date reviews.