Biogas residues (BR) contaminated with potentially toxic metals pose environmental risks to soils and food chains, and strategies are needed to decrease the concentration and bioavailability of potentially toxic metals in BR. Here, metal fractions and removal mechanisms were quantified by synchrotron radiation-based Fourier transform infrared and micro X-ray fluorescence spectromicroscopies on BR and earthworms subject to vermicomposting. Vermicomposting resulted in decreases in concentrations of potentially toxic metals in BR and increases in metal removal efficiencies due to uptake by earthworms. Prior to vermicomposting, Zn, Cu and Pb were associated with N-H, O-H, aromatic C, aliphatic C, and amide functional groups, but following maturation during vermicomposting, metals were associated with N-H, O-H, aliphatic C and polysaccharide functional groups. Following vermicomposting, Zn and Cu were mainly distributed in the dermal portions of earthworms, whereas Pb was more homogeneously distributed among the inner and outer portions of the earthworms, revealing that different metals may have different uptake routes. These findings provide a new strategy for safe utilization of BR by using earthworms via vermicomposting to remove potentially toxic metals and in situ insights into how metals binding and distribution characteristics in BR and earthworms during compost and vermicomposting processes.