Increasing environmental concern forces the reduction in the share of synthetic surfactants in the production of various industries, including mineral processing, by replacing them with more environmentally friendly compounds of biological origin. Several studies on the use of biosurfactants in mineral processing are currently available in the literature, but they contain limited information related to the physicochemistry of these processes. Therefore, this review aims to summarise publications from the last decade related to the role of microorganisms and their metabolic products in mineral surface modification applied in mineral processing. Theoretical principles of bacteria–mineral interactions are presented. Salt-type, sulphide, and oxide minerals were discussed with greater attention to the physicochemistry of biosurfactant–mineral interactions, such as the wettability and surface charge. The advantages and disadvantages of using bacterial cells and surface-active microbial compounds were proposed. The trends and challenges of biomodification in flotation and flocculation were discussed.