Increased temperature as a result of climate change has a direct effect on the functional capacity of microbial communities, but community-wide responses are understudied. This study used tandem mass tag (TMT)-based proteomics to measure protein expression in acid mine drainage biofilms at 40 °C, 43 °C and 46 °C. The expression of proteins that are involved in amino acid metabolism increased substantially across the community at 46 °C, whereas proteins that are involved in carbon fixation showed differential responses, such that these proteins were repressed in two Leptospirillum spp., whereas their abundance increased in a third species. Thus, climate change is likely to have a considerable impact on the contribution of microbial communities to biogeochemical processes.