The increased mining of metals required to meet future demands also generates vast amounts of waste rock that depending on the ore, can contain substantial amounts of metal sulfides. Unconstrained storage of these mining biproducts results in the release of acidic metal laden effluent (termed ‘acid rock drainage’) that causes serious damage to recipient ecosystems. This study investigated the development of 16S rRNA gene based microbial communities and physiochemical characteristics over two sampling occasions in three age classes of rock, from newly mined to > 10 years in a boreal metal sulfide waste repository. Analysis of the waste rocks showed a pH decrease from the youngest to oldest aged waste rock suggesting the development of acid rock leachate. The microbial communities differed between the young, mid, and old samples with increasing Shannon’s H diversity with rock age. This was reflected by the young age microbial community beta diversity shifting towards the mid aged samples suggesting the development of a community adapted to the low temperature and acidic conditions. This community shift was characterized by the development of iron and sulfur oxidizing acidophilic populations that likely catalyzed the dissolution of the metal sulfides. In conclusion, the study showed three potential microbial community transitions from anaerobic species adapted to underground conditions, through an aerobic acidophilic community, to a more diverse acidophilic community. This study can assist in understanding acid rock drainage generation and inform on strategies to mitigate metal and acid release.