The commercial production of the β-carotene, phycocyanin, and astaxanthin pigments from the microalgae Dunaliella salina, Arthrospira platensis, and Haematococcus pluvialis stands out in the microalgae market. These species are the market darlings due to their unique ability to accumulate significant quantities of these pigments, guaranteeing a consistent supply of this valuable ingredient for an infinity of commercial applications. However, like all microalgae-based processes and products, the upstream and downstream steps are energy-intensive, and consequently, the carbon footprint does not go unnoticed. But despite this, by examining carbon emissions from the life cycle of the microalgae-based pigments, it is possible to plot a roadmap for preventing and removing part of the carbon emissions from unit operations and, in doing so, it is possible to take advantage of opportunities of the carbon market. Given this, the chapter aims to shed light on three fundamental aspects: (i) the carbon footprint, (ii) strategies to mitigate it, and (iii) the potential for commercializing the results of carbon mitigation of microalgae pigments production. Examining these points provides a comprehensive understanding of the pigment production chain, from its origin to the factory gate. The insights presented can help the microalgae industry move toward achieving net-zero emissions.