Indirubins are natural-plant secondary metabolites that belong to the family of indigoids. Indirubin and its derivatives play a vital role in the fields of dyes and medicinal chemistry. Indirubin is an active ingredient of traditional Chinese medicine that is used to treat chronic myeloid leukemia. Studies revealed that indirubin and its derivatives have hemostatic, antipyretic, anti-inflammatory, antibacterial, and antiviral properties. Bioactive indirubin-derivatives have been produced for pharmaceutical applications by leveraging the costly and hazardous chemical synthesis routes. Currently, it is mainly used for the clinical treatment of chronic myeloid leukemia and features the advantages of low toxicity and few side effects. Additionally, studies demonstrated that indirubin-derivatives can act as an immunologically active anti-tumor drug for cancer treatments. This review highlights the potential of green metabolic routes for developing indirubin-derivatives from biomass via microbial approaches. We described the key enzymes, including P450s and other monooxygenases, and the synthetic biology strategies that tailor these enzymes and relevant metabolic pathways in E. coli to funnel biomass-derived substrates to indirubin and its derivatives via a key precursor molecule tryptophan. We also highlighted the chemo-microbial hybrid process to obtain the indirubin-derivative from biomass-derived substrates. The presented sustainable microbial approaches will enable the production of indirubin-derivatives at a commercial scale which can be adapted to the microbial production of other high-value indigoids.