Silica and kaolin are important industrial minerals and are used in various industries. Different physical and chemical methods have been used to purify these minerals . However, such methods are often inefficient, expensive and not environmentally friendly. Therefore, microbial purification approaches are preferred because of their milder environmental behavior, lower energy consumption and capital/operating costs, and for maintaining the crystalline structure of claysMicrobes can function as biosurfactants to selectively flocculate or disperse particles, and do mineral separation. This is achieved by selective adhesion of cells (direct method) or their extracts (indirect method) onto mineral surfaces and altering their surface properties. Therefore, in the present study, Bacillus licheniformis cells and their metabolite were used to change the settling behavior of kaolin and silica powders. Moreover, to perform a more detailed study on the Metabolite, settling effect of its protein and polysaccharide constituents were also investigated separately. Settling tests were planned using a full factorial design of experiments, in which the effects of dispersion pH and mineral concentration using direct and indirect method were investigated and analyzed according to the results of adsorption tests. Generally, it was concluded that using each of the mentioned bioreagents in an appropriate pH range increased kaolin and silica sedimentation, while increasing mineral concentration in the dispersion, substantially dwindled settling efficiency. Also, it was found that the flocculating ability of bacterial metabolite is largely due to its polysaccharides rather than its protein contents. Finally, mineral separations from iron oxides as contaminants using optimum flocculation conditions did not show any promising results.