Evolution occurring over ecological time scales can affect community functions both directly and indirectly, via changes in community composition. This interplay between ecology and evolution makes identifying the role of rapid evolution in shaping the functioning of complex natural communities challenging. We used a methanogenic community from an anaerobic digester to investigate the potential importance of rapid evolution in shaping community methane production. To disentangle evolutionary and ecological processes, we pre-adapted the community to a novel feedstock in laboratory anaerobic fermenters for 6 weeks and then inoculated 1% back into the ancestral community. This allowed the introduction of any within-taxa genetic changes that occurred over the pre-adaptation period, while minimally altering the taxonomic composition of the community. The addition of the pre-adapted inoculum increased biogas production by ~10% over 6 weeks compared to a control treatment without the addition, with the corresponding minor changes in community composition unable to explain this increase. These findings suggest that rapid adaptive evolution can play an important role in shaping the structure and function of natural microbial communities and provide a novel approach to enhancing microbial community functions.