This study deals with anaerobic biotreatments of sediments contaminated with toxic metals carried out in slurry reactor. The sediment samples used for the investigation came from two Italian ports, and they were mainly contaminated with inorganic compounds (zinc, nickel and chromium). The treatments were aimed at assessing the responses of the autochthonous microbial community in relation to the geochemistry of the sediments (mainly organic carbon bioavailability) and the addition of organic and inorganic substrates. It was observed that the bio-available carbon in the sediments can greatly influence microbial growth but without a significant effect on metal mobilization. By contrast, the supply of inorganic nutrients to the sediments did not have a major effect on microbial growth although important changes in metal mobility were observed. Our results provide new insights on the effects of anaerobic biotreatments on changes in metal partitioning in contaminated sediments, highlighting that, under certain conditions, an increase of metals in the more mobile fractions can occur.