Diesel-fueled engines still hold a large market share in the medium and heavy-duty transportation sector. However, the increase in fossil fuel prices and the strict emission regulations are leading engine manufacturers to seek cleaner alternatives without a compromise in performance. Alcohol-based fuels, such as ethanol, offer a promising alternative to diesel fuel in meeting regulatory demands. Ethanol provides cleaner combustion and lower levels of soot due to its chemical properties, in particular its lower level of carbon content. In addition, the stoichiometric operating conditions of alcohol fueled engines enable the mitigation of NOx emissions in aftertreatment stage. With the promise of retrofitting diesel engines to run on ethanol to reduce emissions, the thermal efficiency of these engines remains the primary optimization target. In order to find the optimal ethanol-fueled engine design that maximizes the thermal efficiency, a large design space needs to be investigated using engineering tools. In this study, previous research by the authors on optimizing the design of a single-cylinder ethanol-fueled engine was extended to explore the design space for a heavy-duty multicylinder engine configuration. A heavy-duty engine setup with multiple operating conditions at different engine speeds and loads was considered. A design optimization analysis was performed to identify the potential designs that maximize the indicated thermal efficiency in an ethanol-fueled compression ignition engine. First, a computational fluid dynamics (CFD) model of the engine was validated using experimental data for four drive cycle points. Using a design of experiments (DoE) approach and a parameterized piston bowl geometry, the model was then exercised to explore the relationship among geometric features of the piston bowl and spray targeting angle and indicated thermal efficiency across all tested operating conditions. After evaluating 165 candidate designs, a piston bowl geometry was identified that yielded an increase between 1.3% and 2.2% points in indicated thermal efficiency for all tested conditions, while satisfying the operational design constraints for peak pressure and maximum pressure rise rate. The increased performance was attributed to enhance mixing that led to the formation of a more homogeneous distribution of in-cylinder temperature and equivalence ratio, higher combustion temperatures, and shorter combustion duration. Finally, a Bayesian optimization (BOpt) analysis was employed to find the optimal piston bowl geometry with a fixed spray injector angle for one of the operating conditions. Using BOpt, a piston candidate was identified that resulted in a 1.9% point increase in thermal efficiency from the baseline design, yet only required 65% of the design samples investigated using the DoE approach.