In various natural and engineered systems, mineral–fluid interactions take place in the presence of multiple fluid phases. While there is evidence that the interplay between multiphase flow processes and reactions controls the evolution of these systems, investigation of the dynamics that shape this interplay at the pore scale has received little attention. Specifically, continuum scale models rarely consider the effect of multiphase flow parameters on mineral reaction rates or apply simple corrections as a function of the reactive surface area or saturation of the aqueous phase, without developing a mechanistic understanding of the pore-scale dynamics. In this study, we developed a framework that couples the two-phase flow simulator of OpenFOAM (open field operation and manipulation) with the geochemical reaction capability of CrunchTope to examine pore-scale dynamics of two phase flow and their impacts on mineral reaction rates. For our investigations, flat 2D channels and single sine wave channels were used to represent smooth and rough geometries. Calcite dissolution in these channels was quantified with single phase flow and two phase flow at a range of velocities. We observed that the bulk calcite dissolution rates were not only affected by the loss of reactive surface area as it becomes occupied by the non-reactive non-aqueous phase, but also largely influenced by the changes in local velocity profiles, e.g., recirculation zones, due to the presence of the non-aqueous phase. The extent of the changes in reaction rates in the two-phase systems compared to the corresponding single phase system is dependent on the flow rate (i.e., capillary number) and channel geometry, and follows a non-monotonic relationship with respect to aqueous saturation. The pore-scale simulation results highlight the importance of interfacial dynamics in controlling mineral reactions and can be used to better constrain reaction rate descriptions in multiphase continuum scale models. These results also emphasize the need for experimental studies that underpin the development of mechanistic models for multiphase flow in reactive systems.