Currently, the problem of heavy metals soil pollution is getting increasingly serious in China and bioremediation has received much attention on heavy metals removal from soil. Bio-grouting using iron-based complexes produced by the metabolism of iron bacteria A was conducted to remediate soil polluted artificially by heavy metals Cd²⁺ or Cr³⁺ and the effect of bioremediation was investigated. Results showed that the available contents of Cd²⁺ and Cr³⁺ in soil reduced by 38.6% and 50.5% respectively after bio-grouting once, and reduced by 49.9% and 58.7% after bio-grouting twice. Afterwards, Scanning Electron Microscopy (SEM), X-ray Diffraction (XRD), and Fourier Transform Infrared Spectroscopy (FTIR) were used to identify the composition and structure of the iron-based complexes and to analyze the deposition mechanism of heavy metal. Microscopy analyses showed that the iron-based complexes, which contain Ferrum oxydatum phosphate, Schwertmannite, as well as other substances with excellent flocculation efficiency and large specific surface area, had poor crystalline form, but could fix heavy metals in a contaminated environment through adsorption and co-precipitation.