Metal halide perovskite solar cells (PSCs) demonstrate growing commercialization potential among emerging photovoltaic technologies. However, the potential leakage of heavy metal ions such as Pb(II) and Sn(II) from PSCs poses significant environmental and health threats, yet the environment’s capacity to respond remains unknown. This work pioneeringly reports the environment’s natural remediation potential in addressing the risks of perovskite leakage. We find that environmental waste yeasts can efficiently capture leaked Pb(II) and Sn(II) through a combination of physical and chemical adsorption mechanisms. These perovskite heavy metals are further biotransformed and immobilized. Additionally, our study shows a higher removal rate for Sn ions, revealing enhanced environmental sustainability by applying lead-free perovskite photovoltaics. This work conveys a microbial cleanup strategy for removing perovskite heavy metals from the environment, contributing to the advancing practical implementation of perovskite photovoltaics.