Microbial-derived natural pigments present a promising alternative to synthetic colorants, offering diverse benefits and a more sustainable approach. This review explores the potential of deep eutectic solvents (DESs) as sustainable alternatives for recovering natural pigments derived from microbial sources, addressing the environmental and safety concerns associated with conventional extraction methods. Specifically, the microbial pigments discussed in this work include carotenoids (e.g., fucoxanthin, astaxanthin, canthaxanthin, bacterioruberin, lutein, and beta-carotene), chlorophylls, and phycobiliproteins (e.g., phycocyanin and phycoerythrin). The review covers the fundamental properties and classifications of DESs, emphasizing their versatility and tunability for specific applications. The main stages of downstream processing, including biomass pretreatment, pigment extraction, and purification, are examined in detail, with DESs demonstrating better efficiency and selectivity than traditional solvents. The review also discusses the challenges and opportunities in developing task-specific DESs, optimizing extraction techniques, and achieving scalable, eco-friendly processes. The potential for using DES-based systems to produce ready-to-use pigment-rich extracts is highlighted, creating potentially new applications in food, cosmetics, and pharmaceuticals. The findings underscore the DESs' role in advancing the sustainable production of microbial pigments, and their implications for broader industrial adoption and the needs for further research.