AbstractGeochemically driven alterations of fractures in multi‐mineral media can create altered layers (ALs) at the fracture‐matrix interface. Spatial variations in the AL significantly influence mass transfer across the interface, and the hydraulic and mechanical properties of the fractured medium. A real‐rock based microfluidic experiment reported spatial variations in AL thickness despite the initially smooth fracture surface, suggesting potential effects of matrix heterogeneity on AL development. However, the respective contribution of structural and mineralogical characteristics is still poorly understood. Using the microfluidic experimental data and a micro‐continuum reactive transport model, we systematically evaluated how micro‐porosity and initial mineral texture impact AL development and thus the overall reactive transport behaviors. Our simulation results confirmed that the extent of AL spatial variations, mainly controlled by mineralogical texture, influences the evolution of reaction and permeability in different ways. Accounting for spatial heterogeneity in mineral distribution produces “channeling” structures in ALs and lower overall reaction (by up to 35.6%), but larger permeability increase (by up to 9.8%). The characteristic length of the reactive mineral cluster was observed to dominate the internal texture of ALs. Whereas the presence of micro‐porosity can enhance mineral accessibility via improving connectivity for flow and transport, and lead to both higher bulk reaction, that is, thicker ALs, and permeability enhancement. Considerations of surface roughness with characteristic length on the same order of magnitude as mineral texture did not change the overall development of AL, which further highlights the importance of accounting for rock matrix properties in predicting long‐term evolution of fractured media. The resulting spatial variations of ALs and their impacts on bulk properties, however, are expected to be further complicated by the coupling of chemical and mechanical processes, and may trigger matrix disaggregation, erosion and other mechanisms of fractured media alteration.