The Upper Permian polymetallic, organic-rich Kupferschiefer black shale in the Fore-Sudetic Monocline is acknowledged to be one of the largest Cu-Ag deposits in the world. Here we report the results of the first study of bioweathering of this sedimentary rock by indigenous heterotrophic bacteria. Experiments were performed under laboratory conditions, employing both petrological and microbiological methods, which permitted the monitoring and visualization of geomicrobiological processes. The results demonstrate that bacteria play a prominent role in the weathering of black shale and in the biogeochemical cycles of elements occurring in this rock. It was shown that bacteria directly interact with black shale organic matter to produce a widespread biofilm on the Kupferschiefer shale surface. As a result of bacterial activity, the formation of pits, bioweathering of ore and rock-forming minerals, the mobilization of elements and secondary mineral precipitation were observed. The chemistry of the secondary minerals unequivocally demonstrates the mobilization of elements from minerals comprising Kupferschiefer. The redistribution of P, Al, Si, Ca, Mg, K, Fe, S, Cu and Pb was confirmed. The presence of bacterial outer membrane vesicles on the surface of black shale was observed for the first time. Biomineralization reactions occurred in both the membrane vesicles and the bacterial cells.