This study is dedicated to improving the efficiency of the flamelet-generated manifold (FGM) tabulated chemistry combustion modeling approach for predicting the combustion process in diesel-ignited internal combustion (IC) engines. The primary focus is on reducing table generation time and memory requirements. To accurately predict dual-fuel combustion processes, it is important to model both premixed and non-premixed combustion regimes. However, attempting to include both regimes in a single FGM lookup table leads to significant increases in the table size and generation time. In response, this work proposes a dual-table configuration, with each table dedicated to a specific regime. The solution is then interpolated from these tables based on the calculated combustion regime indicator during the computational fluid dynamics (CFD) simulation. This approach optimizes computational efficiency while ensuring an accurate representation of dual-fuel combustion. Additionally, to establish a cost-effective and accurate 3D CFD simulation workflow, the dual-table FGM methodology is coupled with the partially averaged Navier–Stokes (PANS) turbulence model. The feasibility of the proposed FGM methodology is tested utilizing six chemical kinetics mechanisms with different levels of detail. The results of this study demonstrated that the dual-table approach significantly accelerates table generation time and reduces memory requirements compared to a single table that includes both combustion regimes. Furthermore, 3D CFD simulation results of the dual-fuel combustion process are validated against available experimental data for three engine operating points. The in-cylinder pressure traces and rate of heat release obtained from the 3D CFD simulations employing the FGM PANS methodology show good agreement with experimental measurements, confirming the accuracy and reliability of this modeling approach.