The expansion of the European Union Emission Trading System (EU ETS) to include the maritime sector introduces new carbon cost obligations for shipping companies. This study evaluates the economic and environmental impacts of the EU ETS on bulk carriers by analyzing a range of operational scenarios involving both conventional and alternative marine fuels. The findings demonstrate that transitioning from conventional engines using heavy fuel oil (HFO) to dual-fuel engines results in significant reductions in carbon dioxide (CO2) emissions, averaging 27.15% for liquefied natural gas (LNG) and 20.60% for methanol. However, while LNG usage in gas engines lowers CO2 emissions, it leads to a 23.92% increase in methane emissions, underscoring the trade-offs associated with fuel selection. Economic evaluation through Levelized Cost of Energy (LCOE) reveals that methanol consistently increases LCOE across all fuel and carbon pricing scenarios. LNG and methanol exhibit marginal increases in LCOE relative to HFO. Biodiesel yields moderate increments, whereas bio-LNG and bio-methanol lead to substantial rises in LCOE. The analysis further indicates that incorporating methane and nitrous oxide into the EU ETS could marginally intensify carbon pricing effects, with CO2-equivalent adjustments raising LCOE by up to 3.16%. These results highlight the importance of strategic fuel selection and operational planning to balance economic viability with environmental performance. While alternative fuels contribute to emission reductions, their financial feasibility remains constrained under current EU ETS pricing structures. The insights presented in this study offer valuable guidance for policymakers and industry stakeholders in advancing sustainable decarbonization strategies within the maritime sector.