Amorphous calcium carbonate (ACC) is a precursor of crystalline calcium carbonates that plays a key role in biomineralization and polymorph evolution. Here, we show that several bacterial strains isolated from a Hungarian cave produce ACC and their extracellular polymeric substance (EPS) shields ACC from crystallization. The findings demonstrate that bacteria-produced ACC forms in water-rich environment at room temperature and is stable for at least half year, which is in contrast to laboratory-produced ACC that needs to be stored in a desiccator and kept below 10 °C for avoiding crystallization. The ACC-shielding EPS consists of lipids, proteins, carbohydrates and nucleic acids. In particular, we identified large amount of long-chain fatty acid components. We suggest that ACC could be enclosed in a micella-like formula within the EPS that inhibits water infiltration. As the bacterial cells lyse, the covering protective layer disintegrates, water penetrates and the unprotected ACC grains crystallize to calcite. Our study indicates that bacteria are capable of producing ACC, and we estimate its quantity in comparison to calcite presumably varies up to 20% depending on the age of the colony. Since diverse bacterial communities colonize the surface of cave sediments in temperate zone, we presume that ACC is common in these caves and its occurrence is directly linked to bacterial activity and influences the geochemical signals recorded in speleothems.