This work proposes an optimization approach for capturing carbon dioxide from different industrial facilities to yield an algae-based biorefinery. The proposed approach is based on a distributed system to account for the economies of scale and includes site selection for the processing facilities. Additionally, the model considers optimization for the technologies used in the process stages and different technologies to yield several products. The algae oil that is obtained from each facility can be sent to processing hubs located in the same plant and/or to a central processing unit. The objective function is to minimize the total annual cost for the treatment of flue gases, including the capital and operating costs for the different processing stages and the overall transportation costs associated with the system minus the sales of products plus the tax credit for reducing CO2 emissions. The results show several economic benefits.