Bacterial weathering plays a significant role in rock weathering, yet only a limited number of studies were conducted on this topic. The recent rapid developments in geomicrobiology are expected to increase the pace of research in this area. The extent and duration of the biological weathering processes on mineral and rock samples and minerals preferred by bacteria are still not fully understood due to the wide variety of both bacterial species and rock types. Biological weathering of rock types found in Turkey has also not been studied before. Here, we investigated the effects of two species of bacteria actively contributing to rock weathering on three rock types commonly used as building stone materials in Turkey. Granite, andesite, and limestone samples could interact with Bacillus species (B. subtilis and B. pumilus) in closed system reactors. Samples obtained from these reactors were analysed via scanning electron microscopy (SEM) monitoring to identify morphological features and chemical composition changes. Chemical elements consumed most by bacteria were identified. Changes in the colour index were determined via RGB measurements. The effects of experimental conditions on bacterial growth were monitored via daily optical density measurements. The effects of bacteria on the physical properties of rock samples were also evaluated. B. subtilis and B. pumilus were found to be more aggressive on limestone/andesite and granite, respectively.