Carotenoids have been associated with risk reduction for several chronic diseases, including the association of their dietary intake/circulating levels with reduced incidence of obesity, type 2 diabetes, certain types of cancer, and even lower total mortality. In addition to some carotenoids constituting vitamin A precursors, they are implicated in potential antioxidant effects and pathways related to inflammation and oxidative stress, including transcription factors such as nuclear factor kappa B (NF-κB) and nuclear factor erythroid 2-related factor 2 (Nrf2). Carotenoids and metabolites may also interact with nuclear receptors, mainly retinoic acid receptor/retinoid X receptor (RAR/RXR) and peroxisome proliferator-activated receptors (PPARs) that play a role in the immune system and cellular differentiation. Therefore, a large number of downstream targets are likely influenced by carotenoids, including but not limited to genes, proteins implicated in oxidative stress and inflammation, antioxidant enzymes and cellular differentiation processes. Furthermore, recent studies also propose an association between carotenoid intake and gut microbiota. While all these endpoints could be individually assessed, a more complete/integrative way to determine a multitude of health-related aspects of carotenoids includes (multi)-omics-related techniques, especially transcriptomics, proteomics, lipidomics and metabolomics, but also metagenomics, measured in a variety of biospecimens including plasma, urine, stool, white blood cells or other tissue cellular extracts. In this review, we highlight the use of -omics technologies to assess health-related effects of carotenoids in mammalian organisms and models.