Bio-cemented soils exhibit different microstructures depending on the spatial distribution of the precipitated calcium carbonate crystals with respect to the host granular skeleton. Previous studies have shown that the distribution pattern strongly affects the mechanical response of bio-cemented soils. Therefore, there is a need to quantitatively characterise the microstructure accounting for the various carbonate distribution patterns. While the mechanical coordination number is widely used to link the micro-scale structure to the macro-mechanical response of granular materials, it has limited capacity to describe the mechanical improvements provided by precipitated carbonate particles when different carbonate distribution patterns are explicitly represented. Therefore, a new effective coordination number is presented to account for the various mechanical contributions of different carbonate distribution patterns. The results show that, compared to the mechanical coordination number, the effective coordination number can better describe the mechanical performance of bio-cemented soil with different carbonate distribution patterns.