The science of nutrigenomics addresses genetics and epigenetics concerning the multiple effects of food. It tells how food components cause a modification of gene expression and health status. Nutrition interventions are coupled together with molecular biology, genomics, and bioinformatics. It focuses on how nutrients control epigenetic processes, such as DNA methylation, histone modifications, and non-coding RNA interactions. Some important principles in nutrigenomics are the influence of diet on epigenome maintenance and, thus, cell-specific gene regulation and metabolism pathways. Various nutrients like polyphenols, vitamins, and fatty acids have epigenetic effects that dictate health and disease phenotypes, such as folate and other methyl donors taking part in DNA methylation and bioactive compounds, for example, resveratrol and curcumin that are implicated in histone modification and chromatin remodeling. These epigenetics and nutrients will help in the prevention and pathogenesis of metabolic syndrome, cardiovascular diseases, neurodegenerative diseases, and cancers. Intergenerationally epigenetic inheritance suggests that environmental exposures or dietary patterns could endure individually and be passed on to the heirs. Personalized nutrition becomes extremely necessary when genomics and epigenomics for personal dietary recommendations become operational for the prevention and optimum health state from disease prevention. Technological advancements like high-throughput sequencing and genome-wide association studies (GWAS) and CRISPR-based epigenetic editing have been a gigantic leap for nutrigenomics research when it comes to analyzing the interactions of nutrients with genes with accuracy. Future studies in nutrigenomics will continue unraveling the complexities of gene-nutrient interactions and will most probably lead to new therapies for disease and a better quality of life.