Systems Microbiology is a new way to approach research in microbiology. The idea is to treat the microorganism or community as a whole, integrating fundamental biological knowledge with OMICS research (genomics, proteomics, transcriptomics, metabolomics) and bioinformatics to obtain a global picture of how a microbial cell operates in the community. The oxidative reactions resulting in the extraction of dissolved metal values from ores is the outcome of a consortium of different microorganisms. Therefore, this bioleaching community is particularly amenable for the application of Systems Microbiology. As more genomic sequences of different biomining microorganisms become available, it will be possible to define the molecular adaptations of bacteria to their environment, the interactions between the members of the community and to predict favorable or negative changes to efficiently control metal solubilization. Some key phenomena to understand the process of biomining are biochemistry of iron and sulfur compound oxidation, bacteria-mineral interactions (chemotaxis, cell-cell communication, adhesion, biofilm formation) and several adaptive responses allowing the microorganisms to survive in a bioleaching environment. These variables should be considered in an integrative way from now on. Together with recently developed molecular methods to monitor the behavior and evolution of microbial participants during bioleaching operations, Systems Microbiology will offer a comprehensive view of the bioleaching community. The power of the OMICS approaches will be briefly reviewed. It is expected they will provide not only exciting new findings but also will allow predictions on how to keep the microbial consortium healthy and therefore efficient during the entire process of bioleaching.