Shifts in plant functional groups associated with climate change have the potential to influence peatland carbon storage by altering the amount and composition of organic matter available to aquatic microbial biofilms. The goal of this study was to evaluate the potential for plant subsidies to regulate ecosystem carbon flux (CO2) by governing the relative proportion of primary producers (microalgae) and heterotrophic decomposers (heterotrophic bacteria) during aquatic biofilm development in an Alaskan fen. We evaluated biofilm composition and CO2 flux inside mesocosms with and without nutrients (both nitrogen and phosphorus), organic carbon (glucose), and leachates from common peatland plants (moss, sedge, shrub, horsetail). Experimental mesocosms were exposed to either natural sunlight or placed under a dark canopy to evaluate the response of decomposers to nutrients and carbon subsidies with and without algae, respectively. Algae were limited by inorganic nutrients and heterotrophic bacteria were limited by organic carbon. The quality of organic matter varied widely among plants and leachate nutrient content, more so than carbon quality, influenced biofilm composition. By alleviating nutrient limitation of algae, plant leachates shifted the biofilm community toward autotrophy in the light-transparent treatments, resulting in a significant reduction in CO2 emissions compared to the control. Without the counterbalance from algal photosynthesis, a heterotrophic biofilm significantly enhanced CO2 emissions in the presence of plant leachates in the dark. These results show that plants not only promote carbon uptake directly through photosynthesis, but also indirectly through a surrogate, the phototrophic microbes.