Based on the knowledge obtained from acid mine drainage formation in mine waste environments (tailings impoundments and waste rock dumps), a new methodology is applied to characterize new ore deposits before exploitation starts. This gives the opportunity to design optimized processes for metal recovery of the different mineral assemblages in an ore deposit and at the same time to minimize the environmental impact and costs downstream for mine waste management. Additionally, the whole economic potential is evaluated including strategic elements. The methodology integrates high-resolution geochemistry by sequential extractions and quantitative mineralogy in combination with kinetic bioleach tests. The produced data set allows to define biogeometallurgical units in the ore deposit and to predict the behavior of each element, economically or environmentally relevant, along the mining process.