The sugarcane sector in Brazil has undergone a major modernization in the last thirty years. Embracing the biorefinery concept, this sector is investigating bioproduct diversification and mostly putting a lot of effort and investment on second generation ethanol production. In this context, the investigation of the integration of a third generation biofuel production using microalgae to the sugarcane biorefinery seems an important starting point. This study evaluates the integration of microalgae growth and processing to a sugarcane biorefinery producing first and second generation ethanol using process simulation tools. Microalgae are cultivated using CO2 produced during fermentation of ethanol and it is processed using supercritical fluid extraction technology in order to obtain lipids rich in high added-value compounds, carotenoids. The results showed that the integration of microalgae biomass processing without previously drying with the sugarcane biorefinery is not attractive from the thermo-economic point. When considering the extraction of dried microalgae the extraction process could be thermal integrated to the sugarcane biorefinery producing ethanol without the need of buying external fuel. The amount of CO2 used as solvent to the supercritical fluid extraction was the main factor that influenced the economic viability of the process. When microalgae pretreatment by cell disruption or co-solvent extraction was considered, it was possible to decrease the amount of CO2 used in the process and an increase in process yields was consequently achieved. The use of a co-solvent in the extraction increased in 1.4 and 2.4 times lipids and carotenoids extraction, respectively, and presented a lower investment when comparing with microalgae extraction without cell disruption.