Synthetic colorants have predominated over natural colorants mainly due to their relatively more stable color, larger synthesis scale, and lower manufacturing costs. However, the environmental and health impacts arising from the excess use of these chemicals have brought up increasing demand for natural colorants. Recent advances in microbial metabolic engineering are enabling an increasing number of natural colorants to be manufactured at large scale in a greener and sustainable manner. In this paper, we review the metabolic engineering tools and strategies employed for the microbial production of natural colorants and their derivatives, focusing on the enhanced production of major natural colorants and diversification of natural colorants with more desirable physicochemical properties. Future prospects and challenges are also discussed.