This study investigated the effects of pore structure and environmental factors on microbial community structures in cementitious materials, based on a two-year exposure experiment. Microbial diversity increased significantly in cementitious materials with pore size larger than 0.1 µm. This trend was particularly pronounced in areas exposed to rainfall. Anaerobic Firmicutes were dominant in dense mortar sampler, whereas samplers with coarser pores favored aerobic Actinobacteria and Proteobacteria. Moisture content was identified as the primary environmental factor influencing microbial abundance. These findings suggest that specific microbial groups may serve as indicators of concrete degradation associated with changes in pore structure.