International shipping has extended its decarbonization strategy to reduce greenhouse gas emissions beyond onboard CO2 emissions. Onboard carbon capture and storage systems are being investigated as a potential solution for fossil-fueled ships, however there is a lack of knowledge on the reduction of well-to-wake greenhouse gas emissions that could be enabled. Considering the ambitious emission reduction targets, this may lead to inaccurate estimations of the future fuel mix in the maritime sector and the market share of marine engines. This study defines nine ship propulsion scenarios based on combinations of fossil fuels and marine engines. To better understand the greenhouse gas emission reduction of onboard carbon capture, this study calculates the well-to-wake greenhouse gas intensity of each scenario with and without onboard carbon capture and storage from the ship’s main engine(s). Deploying onboard carbon capture and storage systems notably reduces the tank-to-wake greenhouse gas intensity (54–68 % depending on the scenario). Contrary to onboard emissions, oil-fueled ships with onboard carbon capture and storage are found to be less greenhouse gas intensive and more cost-effective than LNG-fueled ships. The four-stroke oil-fueled engine achieves the lowest well-to-wake greenhouse gas intensity of 38.31 gCO2eq/MJ, while the four-stroke LNG-fueled engine has the highest intensity of 50.34 gCO2eq/MJ. The greenhouse gas emission levels enabled by onboard carbon capture from the main engine would allow fossil-fueled ships to comply with the FuelEU Maritime greenhouse gas intensity requirement until 2044. To be compliant in subsequent periods, onboard carbon capture and storage systems will need to consider carbon capture from the auxiliary boiler and generator and higher capture rate, as well as measures to reduce upstream emissions from fossil fuel production and transport.