Enzyme-induced carbonate precipitation (EICP), which precipitates calcium carbonate within the soil matrix to cement the granular grains, presents a promising bio-mediated approach for scour countermeasures. This study explores the erosion performance of bio-cemented sand in a closed-conduit flume system, investigating the effectiveness of EICP in mitigating scour and reducing erodibility. Various parameters such as curing duration, cementation degrees and urease activities are examined to understand their influence on erosion behaviors. Furthermore, the study incorporates the analysis of calcium carbonate content and crystal microstructure to provide a better understanding on the EICP mechanism in scour mitigation. These results highlight the critical role of the interaction between calcium carbonate content and crystal features in determining the effectiveness of erodibility reduction. As the precipitated amount increases, the cemented soil exhibits enhanced hydraulic erosion resistance, with the erosion mode shifting from particle erosion and aggregated detachment to chunk fracture. In other words, the mode of sediment transport essentially is affected by the variations in crystal size, crystal quantities and deposited morphology. Two predictive formulas for threshold Shields parameter and erosion rate are also developed. Notably, the cemented soil could maintain its stability under an elevated flow of 4 m/s under an EICP treatment with 1 M of urea and calcium chloride, and a curing duration of 24 h. These findings are anticipated to serve as a valuable theoretical foundation for engineering applications.