The shipping sector has been under great pressure since the last decade to improve its environmental footprint, more so recently with the International Maritime Organisation target for a 50% reduction in greenhouse gas emissions by 2050, benchmarked to 2008 levels. These challenging goals have increased the interest towards alternative fuels and ship energy systems that can offer a more sustainable performance. The variety of potential technological solutions along with the multiple criteria employed to evaluate the ship energy systems with respect to sustainability considerations, renders the decision-making process for selecting ship energy systems challenging and highlights the need for dedicated decision support methods. This study presents a state-of-the-art review of the literature on decision support methods for enhancing the ship energy systems sustainability. The trends and gaps in the literature are identified, based on which, recommendations for future research are proposed. This study findings indicate that, among others, further research is needed to adapt more holistic approaches that include safety and reliability indicators as well as the social aspect of sustainability. This review can be beneficial for the maritime industry stakeholders, including policy makers, academics and ship owners/operators.