The present study reports on the effect of Fe2+, Ni2+ and CO2+ on anaerobic bacterial activity and dynamics during anaerobic mineralization of organic matter. Fe2+ stimulated biogas yield and methane content at 37 °C, but inhibited same marginally at low temperatures (10 and 20 °C). Ni2+ and CO2+ inhibited methane production; the toxicity increased with decreasing temperature. Fe2+ stimulated sulfate reducing bacterial (SRB) and methane producing bacterial (MPB) counts while Ni2+ and CO2+ inhibited the same. All the metals had no effect on obligate proton reducing bacterial (OPRB) counts. Fe2+ stimulated, Ni2+ severely and CO2+ appreciably inhibited H2 uptake and acetate/propionate utilization irrespective of presence/absence of sulfate. Thus, Ni2+ and CO2+ inhibited the overall anaerobic degradative process by inhibiting SRB and MPB activity.