Nutrigenomics relates the interaction of nutrients with genes and their subsequent effect on the human body. Bioactive compounds, being the health-beneficial secondary metabolites, have a significant effect on the human genome, which is the basic aim behind this article. This chapter explains the functional role of bioactive compounds, their mode of action on different organs of the body, and overall health effects down to the genome level. The two major features, namely bioaccessibility and bioavailability, are also focused on in-depth to understand the actual efficacy of bioactive compounds in the bloodstream. The ethical concern of human trials is still a hurdle to overcome, and detailed simulation of extraction, encapsulation, and release studies is the need of the hour to carry forward this approach. The chapter gives a generic idea of basic mechanisms involved in the utilization of bioactive compounds towards nutrigenomics and gives future perspectives for better and more precise simulations to validate the approach.