<p>The maritime industry is facing increased pressure to adopt zero or near-zero greenhouse gas (GHG) emission technologies, fuels and energy sources and to reach net-zero GHG emission by or around 2050. Battery-powered electric ferries (BEF) are a sustainable alternative to ships with the diesel power systems, offering environmental and economic advantages for short-sea shipping. When integrated with ship-to-grid (S2G) technology, the BEF can also provide ancillary services, improving the flexibility, stability and resilience of the overall energy system. This study investigates the potential of S2G by modeling future scenarios for ferry operations in the Croatian short-sea shipping sector. A cross-sectoral energy management system (EMS) demonstrated the synergies between the energy system of an island, the ship energy system, the ship operating schedule, the BEF state-of-charge (SOC) and the electricity price in the day-ahead market (DAM). A market-driven smart charging strategy is implemented to evaluate the benefits of S2G in the advanced electricity market. Simulation results indicated differences across scenarios, including increased S2G utilisation linked to extended SOC cycling ranges. These variations affect the availability of power flexibility from BEF for ancillary services. The case study highlights S2G as a viable option for improving the sustainability of both the energy and short-sea shipping sectors. The EMS serves as a universal decision-support tool for researchers, investors and policymakers, highlighting the need for a regulatory framework to facilitate the integration of S2G in the DAM.</p>