The process is more environmentally friendly than traditional extraction methods.  For the company this can translate into profit, since the necessary limiting of sulfur dioxide emissions during smelting is expensive. Less landscape damage occurs, since the bacteria involved grow naturally, and the mine and surrounding area can be left relatively untouched. As the bacteria breed in the conditions of the mine, they are easily cultivated and recycled.
Toxic chemicals are sometimes produced in the process. Sulfuric acid and H ions that have been formed can leak into the ground and surface water turning it acidic, causing environmental damage. Heavy ions such as iron, zinc, and arsenic leak during acid mine drainage. When the pH of this solution rises, as a result of dilution by fresh water, these ions precipitate, forming "Yellow Boy" pollution. For these reasons, a setup of bioleaching must be carefully planned, since the process can lead to a biosafety failure. Unlike other methods, once started, bioheap leaching cannot be quickly stopped, because leaching would still continue with rainwater and natural bacteria. Projects like Finnish Talvivaara proved to be environmentally and economically disastrous.