Microbes play a major role in the global carbon cycle that fuels climate change. But how microbes may in turn respond to climate change remains poorly understood. Here, we collect data from a long-term whole-ecosystem warming experiment at a boreal peatland to address how temperature and carbon dioxide jointly influence protist communities: i.e., abundant and diverse, but poorly understood, microbial Eukaryotes. Protists influence ecosystem function directly through photosynthesis and respiration, and indirectly through predation on decomposers (bacteria, archaea, and fungi). Using a combination of high-throughput fluid imaging and 18S amplicon sequencing, we report climate-induced, community-wide shifts in protist community functional composition (e.g., size, shape, and metabolism) that could alter the overall function of peatland ecosystems. We also show that these responses to warming and elevated carbon dioxide are the result of taxonomic turnover. Surprisingly, our results clearly show strong interactive effects between temperature and carbon dioxide, such that the effects of warming on functional composition are generally reversed by elevated carbon dioxide. These findings show how the interactive effects of warming and rising carbon dioxide could alter the structure and function of peatland microbial food webs: a fragile ecosystem that stores 25% of terrestrial carbon and is increasingly threatened by human exploitation.