In multi‐phase bulk ceramics, the separate influence of individual phases on the overall macroscopic properties can often hardly be studied by purely experimental observations. However, once a realistic microstructure model exists, computer simulations allow for that by varying the properties of individual phases and, thus, for studying their role independently. In the present article, the microstructure of liquid phase sintered silicon nitride ceramics was created using a voxel‐based structure generator. These generated microstructures have been meshed with a special tool so that thermal conductivities and elastic properties of these ceramics could be calculated using standard finite element simulations. Variations of the properties of individual phases were considered in a realistic range for the experimental optimization of silicon nitride ceramics and, therefore, their respective influence on macroscopic properties could be studied. It turns out that a high volume fraction of the primary β‐Si3N4 ‐phase has the largest positive impact on both stiffness and thermal conductivity, whereas the effect of grain shape and anisotropic material properties of the β‐Si3N4 ‐grains is rather low. However, the thermal conductivity of the secondary phase plays a significant role in the overall thermal conductivity, provided that it drops beyond 10 W m·K−1. Nevertheless, experimentally the thermal conductivity of silicon nitride ceramics is dominated by the thermal conductivity of the β‐Si3N4 ‐grains, where the latter is controlled by impurities which can be incorporated into the silicon nitride lattice during sintering. Thus, inverse simulation can be used as a powerful tool to investigate individual phase properties in multiphase ceramics, for example, estimating a decreased thermal conductivity of the primary phase (β‐Si3N4 ‐grains).