Accurate estimation of contaminant transport in cementitious material using numerical tools plays a key role in the risk assessments of nuclear waste disposal. At the pore scale, the increase of microbial activity, such as microbially induced calcite precipitation on cementitious material, causes changes in solid surface topography, pore network geometry, and pore water chemistry, which affect contaminant transport at the core scale and beyond. Consequently, a meaningful estimation of contaminant migration in the subsurface requires a pore-scale investigation of the influence of microbial activity on transport processes. In this study, a pore-scale reactive transport model is presented to simulate the physicochemical processes resulting from microbially induced calcite precipitation on a cement surface. Numerical investigations focus on modeling the reactive transport in a two-dimensional flow-through cell. The model results are validated by experimental data showing an increase in pH and a decrease in calcium concentration due to microbially induced calcite precipitation. Our results show heterogeneous calcite precipitation under transport-limited conditions and homogeneous calcite precipitation under reaction-limited conditions, resulting in non-uniform and uniform changes in the material surface topography. Moreover, power spectral density analysis of the surface data demonstrates that microbially induced calcite precipitation affects the surface topography via both general changes over the entire frequency and local modifications in the high-frequency region. The sensitivity studies provide a comprehensive understanding of the evolution of surface topography due to the microbially induced calcite precipitation at the pore scale, thus contributing to an improved predictability of contaminant transport at the core scale and beyond.