Ecosystem engineers are organisms able to modify their environment by changing the distribution of materials and energy, with effects on biotic and abiotic ecosystem components. Several ecosystem engineers are known, but for most of them the mechanisms behind their influence are poorly known. We detail the role of bats as ecosystem engineers in iron ore caves in the Carajás National Forest, Brazilian Amazonia, an area with > 1,500 caves, some holding ~150,000 bats. We analyzed the chemical composition of guano deposits in bat caves, radiocarbon-dated those deposits, and elucidated the chemical mechanisms involved and the role the bat guano has on modifying those caves. The insect-composed guano was rich in organic matter, with high concentrations of carbon, nitrogen, phosphorus pentoxide and ferric oxide, plus potassium oxide, calcium and sulfur trioxide. Radiocarbon dating indicated guano deposits between 22,000 and 1,800 years old. The guano pH was mainly acid (from 2.1 to 5.6). Percolating waters in those bat caves were also acid (pH reaching 1.5), with the presence of phosphate, iron, calcium, nitrate and sulfate. Acid solutions due to guano decomposition and possible microbial activity produced various forms of corrosion on the caves´ floor and walls, resulting in their enlargement. Bat caves or caves with evidence of inactive bat colonies had, on average, lengths six times larger, areas five times larger, and volumes five times bigger than the regional average, plus more abundant, diversified and bigger speleothems when compared with other caves. In an example of bioengineering, the long-term presence of bats (> 22,000 years) and the guano deposits they produce, mediated by biological and chemical interactions over millennia, resulted in very unique ecological, evolutionary and geomorphological processes, whose working are just beginning to be better understood by science. However, the current expansion of mineral extraction activities coupled with the loosening of licensing and cave protection rules is a real conservation threat to the bat caves in Carajás. The destruction of those caves would represent an unacceptable loss of both speleological and biological heritage and we urge that, whenever they occur, bat caves and their colonies must be fully protected and left off-limits of mineral extraction.