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This study explores the feasibility of using a sustainable lignin-based fuel, consisting of 44 % lignin, 50 % ethanol, and 6 % water, in conventional compression ignition (CI) marine engines. Through experimental evaluations on a modified small-bore CI engine, we identified the primary challenges associated with lignin-based fuel, including engine startup and shutdown issues due to solvent evaporation and lignin solidification inside the fuel system, and deposit formation on cylinder walls leading to piston ring seizure. To address these issues, we developed a fuel switching system transitioning from lignin-based fuel to cleaning fuel with 85 vol% of acetone, 10 vol% of water and 5 vol% of ignition improving additive, effectively preventing system clogs.