Microalgae are the cell factories of a plethora of secondary metabolites including natural pigments viz. chlorophylls, carotenoids, and phycobiliproteins. Owing to their several functional attributes, these pigments have found applications in analytical, nutraceutical, pharmaceutical, and cosmeceutical industries. In spite of their inherent metabolic capacities, the low pigment yield along with high processing cost not only makes the entire process economically unfeasible, it also limits its useful application. Several studies were conducted to increase biopigments accumulation by manipulating the growth parameters of microalgae. In recent decades, strain improvement via genetic and metabolic engineering approaches has also demonstrated remarkable improvement in the production capacities of microalgae making the prospect of cost-efficient large-scale production realizable. Advances in the next generation sequencing technologies and with the advent of multi-omics analyses viz. transcriptomics, proteomics, and metabolomics, it has been possible to decipher the bottleneck reactions of key biosynthetic pathways for the target molecule/s. Additionally, metabolome profiling either static or dynamic can assist in understanding the complex metabolic network under normal as well as stress conditions to pinpoint the rate-limiting step of any process, which can then be targeted for designing genetic engineering experiments for higher growth and metabolite yield. In this context, this chapter initially highlights the industrial applications of microalgal pigments and their biosynthetic pathways. It further heads to review the genetic engineering strategies deployed in enhanced pigment production and the latest research efforts being made so far in metabolomics-assisted strain engineering. The chapter concludes by emphasizing the major limitations and their possible resolution related to microalgal pigment production.