Nowadays, marine propulsion systems based on thermal machines that operate under the diesel cycle have positioned themselves as one of the main options for this type of applications. The main comparative advantages of diesel engines, compared to other propulsion systems based on thermal cycle engines, are the low specific fuel consumption of residual fuels, and their higher thermal efficiency. However, its main disadvantage lies in the emissions produced by the combustion of the residual fuels, such as carbon dioxide (CO2), sulfur oxide (SOx), and nitrogen oxide (NOx). These emissions are directly related to the operating conditions of the propulsion system. Over the last decade, the International Maritime Organization (IMO) has adopted a series of regulations to reduce CO2 emissions based on the introduction of an Energy Efficiency Design Index (EEDI) and an Energy Efficiency Operational Indicator (EEOI). In this context, adding a Shaft Generator (SG) to the propulsion system favoring lower EEDI and EEOI values. The present work proposes a selective control system and optimization scheme that allows operating the shaft generator in Power Take Off (PTO) or Power Take In (PTI) mode, ensuring that the main engine operates, always, at the optimum fuel efficiency point, thus ensuring minimum CO2 emissions.