The aim of this work is to optimize the conceptual design of an amine-based carbon dioxide (CO2) separation process for Enhanced Oil Recovery (EOR). A systematic approach is applied to predict the economic profitability of the system while reducing the environmental impacts. Firstly, we model the process with UniSim and determine the governing degrees of freedom (DoF) through a sensitivity analysis. Then, we proceed with the formulation of the economic problem, where the employment of econometric models allows us to predict the highest dynamic economic potential (DEP). In the second part, we apply the Waste Reduction (WAR) algorithm to quantify the environmental risks of the studied process. This method is based on the minimization of the potential environmental indicator (PEI) by using the generalization of the Waste Reduction algorithm. Results show that the CO2 separation plant is promising in terms of economic revenues. However, the PEI value indicates that the higher the profitability, the larger the environmental risk. The optimal value of the DEP corresponds to 0.0274 kmol/h and 60 °C, with a plant capacity according to the mole flow rate of the produced acid gas. In addition, the highest environmental risk is observed at the upper bounds of the DoF.