Bio-energy systems with carbon capture and storage (BECCS) will be essential if countries are to meet the gas emission reduction targets established in the 2015 Paris Agreement. This study seeks to carry out a thermodynamic optimization and analysis of a BECCS technology for a typical Brazilian cogeneration plant. To maximize generated net electrical energy (MWe) and carbon dioxide CO₂ capture (Mt/year), this study evaluated six cogeneration systems integrated with a chemical absorption process using MEA. A key performance indicator (gCO₂/kWh) was also evaluated. The set of optimal solutions shows that the single regenerator configuration (REG1) resulted in more CO₂ capture (51.9% of all CO₂ emissions generated by the plant), penalized by 14.9% in the electrical plant’s efficiency. On the other hand, the reheated configuration with three regenerators (Reheat3) was less power-penalized (7.41%) but had a lower CO₂ capture rate (36.3%). Results showed that if the CO₂ capture rates would be higher than 51.9%, the cogeneration system would reach a higher specific emission (gCO₂/kWh) than the cogeneration base plant without a carbon capture system, which implies that low capture rates (<51%) in the CCS system guarantee an overall net reduction in greenhouse gas emissions in sugarcane plants for power and ethanol production.