Environmental and energy sustainability concerns have catalyzed a global transition toward renewable biofuel alternatives. Among these, biodiesel stands out as a promising substitute for conventional diesel in compression-ignition engines, providing compatibility without requiring modifications to engine design. A comprehensive understanding of biodiesel’s physical properties is crucial for accurately modeling fuel spray, atomization, combustion, and emissions in diesel engines. This study focuses on predicting the physical properties of PODL20 and EB100, including liquid viscosity, density, vapor pressure, latent heat of vaporization, thermal conductivity, gas diffusion coefficients, and surface tension, all integrated into the CONVERGE CFD fuel library for improved combustion simulations. Subsequently, numerical simulations were conducted using the predicted properties of the biodiesels, validated by experimental in-cylinder pressure data. The prediction models demonstrated excellent alignment with the experimental results, confirming their accuracy in simulating spray dynamics, combustion processes, turbulence, ignition, and emissions. Notably, significant improvements in key combustion parameters, such as cylinder pressure and heat release rate, were recorded with the use of biodiesels. Specifically, the heat release rates for PODL20 and EB100 reached 165.74 J/CA and 140.08 J/CA, respectively, compared to 60.2 J/CA for conventional diesel fuel. Furthermore, when evaluating both soot and NO_x emissions, EB100 displayed a more balanced performance, achieving a significant reduction in soot emissions of 34.21% alongside a moderate increase in NO_x emissions of 45.5% compared to diesel fuel. In comparison to PODL20, reductions of 20.4% in soot emissions and 3% in NO_x emissions were also noted.