Microalgae pigments comprise a group of industrially high-value bioproducts, whose commercial value entails their use as a primary source of cosmetics, biofuels, food supplements, nutraceuticals, antioxidants, and therapeutic agents. The versatility of microalgae and their metabolic dynamics constitute an avenue for research in the omics era, with increased discovery of novel pigment derivatives from various recipes. Given similar biosynthetic pathways, classes of pigments share common chemical fingerprints that suggest closely related extraction, purification and analytical methods. However, the spectrum of genomic diversity across various microalgae groups significantly influences the metabolic repertoire, which is pretty much dependent on physicochemical conditions. Thus, the application of omics approaches offers opportunities to decipher genomic structures and pipelines for upstream and downstream metabolic orchestration of the most relevant pigment backbones and/or their final products. We hereby discuss such methods spanning from core genome and accessory genome analysis, transcriptome and proteome profiling as well as diverse methodological workflows for enhancement and analysis of metabolomes, emphasis given to pigments. We further pinpoint the opportunities and challenges for each of the omics components along with the trajectory of global commercialization of microalgae pigments.