Strict regulations for carbon emissions from ships are introduced by the IMO and the EU. Various emission mitigation measures and low-emission fuel strategies provide solutions to reduce carbon emissions. This paper compares emission mitigation measures and low-emission fuel strategies for short-sea ships, within the constraints of regulatory compliance. Furthermore, cost sensitivity of measures to fuel, EU ETS and TCE price are compared. The results support shipowners and financiers in making robust investment decisions, and provide insight into the effects of regulatory incentives to regulators.