In Australia, the search for new ore is focused under cover. In these deeply weathered terrains, geochemical and mineralogical dispersion halos surrounding the emplaced ore should contain biological targets for exploration, even with ‘inert’ materials, e.g., the biogeochemical cycling of gold that can produce a variety of materials (colloidal and octahedral gold). Regarding metal extraction, microbiology has important environmental consequences in the generation of acid mine (rock) drainage, damaging 10’s of thousands of km of streams globally and is important in bioleaching, producing 15% of the world’s copper. The role of geomicrobiology should be further exploited in bioleaching of low-grade ore or mine tailings, further reducing the environmental impacts of mining. These soluble metals can be subsequently recovered via the application of acidophilic sulfate reducing bacterial bioreactors precipitating metal sulphides, integrating mine water remediation with selective biomineralisation. With respect to remediation, we are looking at iron ore waste stabilisation and mineral carbonation. Supergene enriched iron ore deposits are typically protected by a goethite-cemented ferruginous duricrust layer (canga). In these deposits, the canga forms extensive deposits blanketing ancient erosion surfaces, is tough, moderately hard, well consolidated, permeable and very resistant to erosion and chemical weathering, protecting the relatively soft enriched iron ore below. This protective canga horizon is therefore, essential to supergene iron ore enrichment and formation of high-grade iron ore. Active, biogeochemical iron cycling is essential for the ‘self’ healing cementation/re-cementation occurring in canga, which should be exploited for the remediation of iron mine sites, post-mining. Adding value to mine waste, biogenic magnesium carbonate mineral precipitation from fine-grained Mg-rich tailings generated by mining operations could potentially offset net mining greenhouse gas emissions. As a proof of concept, cyanobacteria in a wetland bioreactor enabled the precipitation of magnesite (MgCO3), hydromagnesite [Mg5(CO3)4(OH)2·4H2O], and dypingite [Mg5(CO3)4(OH)2·5H2O] from acid leached ultramafic mine tailings.