With the increase in the prevalence of food-related diseases, there is a growing interest in unraveling the effect food might have on human health. A better vision of how food is broken down in the gastrointestinal tract and further metabolized is essential to clarify this link. The recent development of the ‘omics’ technologies now allows a more comprehensive view of the food-derived compounds released in the gut during digestion and the metabolites present in body fluids after intestinal absorption. The objective of the present paper is to give an overview on the latest research describing the digestion process and its relationship with food bioactivity using different ‘omics’ technologies. It emphasizes the complementarity of the ‘omics’ disciplines, i.e. transcriptomics, proteomics, metabolomics, etc. (gathered under the more generic term of ‘foodomics’) and the added value of integrating such datasets.