Emission reduction is one of the major challenges of our time and is driving the development of future engine systems, leading to the use of renewable fuels in combination with advanced combustion modes such as dual-fuel operation. To optimize the performance and reliability of these engine systems, predictive three-dimensional CRFD simulations of the combustion chamber provide a powerful and efficient tool to gain detailed insight into the characteristics of spray formation, mixing, and ignition/combustion processes. The work presented demonstrates the implementation of a newly developed workflow that independently models the ignition of the pilot spray and the combustion of the main fuel, thus providing increased computational efficiency compared to the use of other established combustion models, while at the same time improving the adaptability to different fuel types. The accuracy of the simulation was evaluated against experimental data from an optically accessible test bench under engine-like conditions, allowing comparison of mixture formation, ignition, and combustion. Excellent agreement was found for the application of pilot ignition of ammonia and methane by micro diesel sprays over a range of operating conditions. In addition, the versatility of the developed methodology was demonstrated through simulations involving blends of the primary fuel with hydrogen (H2). This highlights the ability of the implemented workflow to handle and accurately predict the combustion characteristics when the composition of the primary fuel is modified.