Biogrouting has been proposed for improving mechanical properties of soils and rocks, whose performance greatly depends on the location of biocement at pore-scale. To enhance the performance of biogrouting, many strategies were proposed, including the addition of assistants, controlling curing moisture degree, and flocculation of bacteria. Clay is one such assistant which has been proven to be effective, with an assumption of increasing active biocement, i.e. those located between soil particles. In this work, we employed microfluidics to directly observe whether clay minerals can certainly control the location of precipitates and how they function. First of all, the capacity of bentonite and kaolin for adsorbing bacteria were investigated. Then, the location of CaCO3 crystals with and without clay minerals were visually observed using microfluidics. Pore-filling ratios and CaCO3 ratios, which are closely related to permeability and strength of biocemented soils, were quantitatively analyzed from collected images. Finally, the effects of bentonite and kaolin and their dosages on the location of biocement were comprehensively discussed. The results demonstrated that the performance of bentonite and kaolin on adsorbing bacteria and regulating biocement location is distinct due to differences in the morphologies of clays. These findings can help us to improve biogrouting performance on soil stabilization and propose new strategies in various practical applications, such as CO2 sequestration, heavy metal remediation, and oil recovery enhancement, all with a foundational understanding of their mechanisms.