Conventionally, physico-chemical methods are used in mineral processing for recovering value minerals from ores. The ageing of ore processing tailings and waste rocks, and mining tailings contamination by chemical reagents constitute a major threat to the environment. It is imperative to develop novel economically more efficient and environmentally benign methods of flotation and waste processing, exploiting the intriguing and exciting ability of bacteria to selectively modify the surface properties of solids. Microorganisms have not only facilitate hydrometallurgical leaching operations but have also show a great promise in mineral beneficiation processes such as flotation and flocculation. Several laboratory investigations revealed that microorganisms could function similar to traditional reagents. Microorganisms have a tremendous influence on their environment through the transfer of energy, charge, and materials across a complex biotic mineral-solution interface. The bio-modification of mineral surfaces involves the complex action of microorganism on the mineral surface. The manner, in which bacteria affect the surface reactivity and the mechanism of bacteria adsorption, is still unknown and accumulation of the primary data in this area is only starting. The bio-flotation and bio-flocculation processes concern the mineral response to the bacterium presence, which is essentially interplay between microorganism and the physicochemical properties of the mineral surface, such as the atomic and electronic structure, the net charge/potential, acid-base properties, and wettability of the surface. There is an urgent need for developing basic knowledge that would underpin biotechnological innovations in the natural resource (re)processing technologies that deliver competitive solutions.