Natural soil deposits are typically heterogeneous, leading to changes in solution permeation patterns within heterogeneous soils compared to those in homogeneous soils when employing Microbially Induced Carbonate Precipitation (MICP) for soil stabilization. Consequently, estimating the performance of MICP in natural soils solely based on studies in homogeneous soils, as commonly practiced in the past, may not be accurate. In this study, we aimed to investigate the MICP grouting processes in heterogeneous soils with varying levels of heterogeneity under different injection rates. Heterogeneous soils were prepared by connecting two distinct specimens of varying particle sizes through a shared inlet. The permeation patterns and permeabilities were assessed to analyze their correlation. The conversion efficiency and CaCO3 contents were measured to evaluate the efficiency of MICP in stabilizing heterogeneous soils. The results revealed that solution permeation may be primarily influenced by the permeability differences between the two soils, with additional effects from heterogeneity levels and injection rates. Furthermore, using a similar injection strategy as in homogeneous soils in heterogeneous soils could result in preferential flow, leading to non-uniform cementation and wastage of materials. Finally, potential measures were proposed to address these issues, such as monitoring bacterial and reactant concentrations in effluents.