Microorganisms have developed various mechanisms to deal with metals, thus providing numerous tools that can be used in biohydrometallurgical processes. “Biomining” processes—including bioleaching and biooxidation processes—facilitate the degradation of minerals, accompanied by a release of metals. These processes are especially attractive for low-grade ores and are used on an industrial scale mainly for sulfidic ores. In biosorption processes, biomass or certain biomolecules are used to bind and concentrate selected ions or other molecules from aqueous solutions. Biosorptive materials can be an environmentally friendly and efficient alternative to conventional materials, such as ion exchange resins. Other interesting mechanisms are bioaccumulation, bioflotation, bioprecipitation, and biomineralisation. Although these processes are well-known and have been studied in detail during the last decades, the recent strong progress of biotechnologies (e.g., genetic engineering and molecule design), as well as their combination with novel developments in material sciences (e.g., nanotechnologies) facilitate new strategies for the application of biotechnologies in mineral processing. The article gives a summary of current activities in this field that are being performed in our group.