Anaerobic co-digestion of food waste and biosolids was carried out in sequential batch and single-stage batch systems in four treatments. Methane yield, which was used as a functional process parameter, differed between treatments, with the single-stage batch system generating lower volumes than the sequential batch systems. Volatile fatty acid (VFA) concentrations and pH in the leachate also differed between treatments. VFA concentrations were highest and methane generation yields lowest in the single-stage batch system in comparison to the sequential batch systems. The anaerobic microbial community structure of the domains Archaea and Bacteria, determined by denaturing gradient gel electrophoresis, differed between treatments and was correlated to a number of environmental parameters such as pH, VFA concentration and methane generation rate. Methane generation rate was significantly correlated to the community structure of Bacteria but not Archaea. This indicated that the substrates that are produced by acetogens (Bacteria) are important for the growth and community structure of the methanogens (Archaea). Community structure of Archaea changed over time, but this had no observable effect on functional ability based on methane yields. Microbial diversity (H') was shown to be not important in developing a functionally successful anaerobic microbial community.