Diagenetic changes in sedimentary basins may alter hydrocarbon reservoir quality with respect to porosity and permeability. Basins with magmatic intrusions have specific thermal histories that at time of emplacement and in the aftermath have the ability to enhance diagenetic processes. Through diagenesis the thermal conductivity of rocks may change significantly, and the transformations are able to create hydrocarbon traps. The present numerical study quantified the effect of magmatic intrusions on the transitions of opal A to opal CT to quartz, smectite to illite and quartz diagenesis. We also studied how these chemical alterations and the sills themselves have affected the way the subsurface responds to stresses. The modeling shows that the area in the vicinity of magmatic sills has enhanced porosity loss caused by diagenesis compared to remote areas not intruded. Particularly areas located between clusters of sills are prone to increased diagenetic changes. Furthermore, areas influenced by diagenesis have, due to altered physical properties, increased stress accumulations, which might lead to opening of fractures and activation/reactivation of faults, thus influencing the permeability and possible hydrocarbon migration in the subsurface. This study emphasizes the influence magmatic intrusions may have on the reservoir quality and illustrates how magmatic intrusions and diagenetic changes and their thermal and stress consequences can be included in basin models.