In this study, we investigated the Cr(VI) uptake mechanism in an indigenous Cr(VI)-tolerant bacterial strain –Bacillus cereus through batch and microscopic experiments. We found that both the cells and the supernatant collected from B. cereus cultivation could reduce Cr(VI). The valence state analysis revealed the complete transformation from Cr(VI) into Cr(III) by living B. cereus. Further X-ray absorption fine structure and Fourier transform infrared analyses showed that the reduced Cr(III) was coordinated with carboxyl and amido functional groups from either the cells or supernatant. Scanning electron microscopy and atomic force microscopy observation showed that noticeable Cr(III) precipitates were accumulated on bacterial surfaces. However, Cr(III) could also be detected in bacterial inner portions by using transmission electron microscopy thin section analysis coupled with energy dispersive X-ray spectroscopy. Through quantitative analysis of chromium distribution, we determined the binding ratio of Cr(III) in supernatant, cell debris and cytoplasm as 22%, 54% and 24%, respectively. Finally, we further discussed the role of bacterium-origin soluble organic molecules to the remediation of Cr(VI) pollutants.