Investigating fracture evolutions triggered by chemical interactions in caprocks of CO2 storage sites is of great importance when caprock integrity is concerned. Mineral heterogeneity is one of the factors affecting fracture evolution. We present results from flow-through experiments deploying a unique high pressure geo-material microfluidic cell to monitor the fracture evolution of four carbonate-rich caprocks: (1) a homogeneous carbonate-rich sample, (2) a heterogeneous carbonate-rich sample, (3) a heterogeneous carbonate-rich shale sample, and (4) a heterogeneous carbonate-rich organic shale sample, representing different levels of mineral heterogeneity. The results show rather smooth fracture wall dissolution for the homogeneous rock sample. For the heterogeneous sample without shale, however, an altered layer is formed around the fracture that leads to an increase in the fracture roughness. Chemical analyses of effluent solutions demonstrate a decrease in the bulk dissolution rate of calcite over time at a constant flow rate. For the two carbonate-rich shale samples, visual observations using optical microscopy showed little changes in fracture dissolution, although analysis of effluent chemistry confirmed calcite dissolution.