The agro-industrial processing and post-harvesting downstream products generate massive volumes of waste which, if disposed and released unprocessed, can cause environmental pollution. Due to their rich chemical composition, these residues could be implemented as fermentative substrates for obtaining value-added products. Among these, natural microbial pigments are gaining more attraction as alternatives to synthetic ones, with their production considered eco-friendly and biocompatible. Agro-industrial waste-based bio-refineries to produce microbial pigments can represent a suitable approach for both the reduction of environmental pollution, as well as for providing a sustainable framework for addressing bioeconomy. This chapter aims to give an overview of the main microorganisms used for agro-industrial waste valorization for pigment production through a biotechnological process from a circular economy point of view. Moreover, the main drawbacks of the implementation of these residues are discussed.