Mineral precipitation affects the pore structure and thus transport properties of porous media. In this study, we investigated the pore‐scale dynamics of precipitation in diffusion controlled systems and the resulting impacts on the effective diffusivity, using a micro‐continuum reactive transport model. Forty 2D pore structures representing both idealized and realistic geometries were simulated with consideration of different precipitation scenarios and rates. A homogeneous nucleation scenario reproduced patterns observed in previous experimental study showing mixing‐induced precipitation, and a surface growth scenario captured the pattern for mineral precipitation on a substrate with the same or similar mineral structures. In all cases, local precipitation resulted in the reduction in the average porosity of the domain (Φ) until the cessation of diffusive transport and the termination of precipitation. The minimum porosity reached was referred to as the critical porosity (Φc). The effective diffusivity (Deff) decreased with Φ and dropped sharply to effectively zero, i.e. the critical effective diffusivity (Deffc), as Φc was reached. These pore‐scale dynamics can be captured by a revised Φ−Deff relationship that explicitly considers the critical porosity and the corresponding effective diffusivity, and the pre‐exponential coefficient and the exponent of the relationship varied with initial pore structure and the precipitation kinetics. Overall, the homogeneous nucleation scenario results in systematically larger Φc and coefficients that give a sharper decrease in diffusivity as Φc is approached, compared to the surface growth scenario. The revised relationship was also implemented at continuum scale and used to examine column scale diffusivity change and reactions.