Since microalgae utilize carbon dioxide as a nutrient to perform photosynthesis, carbon dioxide is a confirmed essential component for microalgae growth. A suitable reactor type, specialized lighting, carefully controlled nutrients, and precise mixing and control of pH, temperature, and contaminants are all necessary for the careful design of a microalgae photobioreactor. This chapter has addressed the engineering and design of microalgae-based bioreactors for carbon sequestration and valorization of microalgae biomass in biorefineries. Along with the important enzymes in carbon fixation, it also describes the principles of carbon sequestration in microalgae. By fostering economic viability, promoting sustainable industrial practices, and aligning with climate change mitigation goals, supportive policies and public-private partnerships position microalgae bioreactors as a key tool for global sustainability. The use of microalgae as a carbon sequestration technology provides a multifaceted approach to addressing the climate crisis, while also valorizing microalgae biomass in bioreactors for the production of biofuels and high-value products.