Microalgae stand out as a valuable source of carotenoids, with potential applications in various industrial sectors. Cultivating microalgae in wastewater emerges as an alternative to mitigate the high costs associated with the synthetic production of these compounds while contributing to sanitation resource recovery. Previous studies demonstrated the potential for obtaining lutein and betacarotene from biomass cultivated in domestic sewage and agro-industrial effluent. This study conducted comprehensive economic and life cycle analyses to evaluate cultivation reactors (high-rate pond and hybrid system) and extraction methods (ethyl acetate solvent and supercritical fluid) to acquire 1 kg of carotenoids efficiently. For all evaluated scenarios, higher environmental impacts were observed in the Human carcinogenic toxicity category and human health environmental damage associated with ethyl acetate and electricity consumption. Ethyl acetate also stood out with higher costs. The high-rate pond and hybrid system showed similar environmental impacts in scenarios with ethyl acetate extraction; however, when supercritical fluid was used, cultivation in the first reactor resulted in 2.2–6.2 times lower environmental impacts in Midpoint categories. Regarding the extraction method, the use of supercritical fluid demonstrated superior economic and environmental performance despite registering a 53% higher energy consumption than solvent extraction. Thus, for the viability of obtaining carotenoids from microalgae biomass, we recommend that two-stage cultivation approaches, incorporating solvent recovery steps and biomass valorization in a cascade manner within a biorefinery context, be considered in future studies.