In order to quantify the economic and environmental impact of technology selection in ship power systems, four different battery-supported hybrid configurations including diesel and gas combustion engines, as well as natural gas fueled solid oxide fuel cells (SOFCs) are modeled and analyzed. The investigations include component investments, maintenance and operational costs, as well as the components’ and fuels’ carbon footprints, operational greenhouse gases and other relevant emissions. Dynamic energy system models are used to derive economically optimal system designs for an appropriate technology comparison in a cruise ship case study. The assessment is conducted for a cruise ship case study with technology parameters for the near future and 2050. Results indicate that the auxiliary power system based on diesel combustion is inferior both economically and environmentally compared to SOFCs or gas combustion engines. While latter are the most cost efficient, SOFC application provides an environmental improvement without the need for a new fuel such as hydrogen. In a final outlook for the year 2050, SOFCs economically overtake gas combustion engines on the condition that their investment costs decrease and synthetic fuels are introduced to the market as a low emission solution.