<p>Microbial pigments have been gaining prominence as sustainable alternatives to synthetic dyes, which are often associated with environmental impacts and potential health risks. A wide range of microorganisms, including bacteria, fungi and yeasts, are capable of producing pigments of industrial interest. Despite their potential, large-scale production still faces challenges related to cultivation costs and, in particular, extraction steps, which traditionally rely on the use of organic solvents and may present low yields and limited sustainability. In this context, the use of agro-industrial residues as alternative nutrient sources for microbial growth and pigment biosynthesis emerges as a promising strategy for sustainable valorisation, contributing to reduced production costs, mitigation of environmental impacts and strengthening of the circular bioeconomy. However, the recovery of microbial pigments remains a technological obstacle, as many of these compounds are intracellular or associated with cellular structures, making extraction and purification challenging and affecting industrial feasibility. To overcome these limitations, recent advances have focused on improving extraction techniques in order to increase yield, purity and sustainability. This review addresses the main microbial pigments and their producers, highlighting the potential of agro-industrial residues for sustainable production. In addition, it synthesises recent advances in extraction strategies, emphasising approaches that combine efficiency, reduced environmental impact and economic viability. In an integrated perspective, the discussion demonstrates that the combination of low-cost substrates and more sustainable extraction technologies represents a promising pathway to expand production and meet the growing demand for natural colourants in the food, cosmetic and pharmaceutical industries.</p>