We currently lack a robust framework of theoretical predictions and experimental tests of how invertebrate community size-structure in freshwater ecosystems may change due to rising temperatures. A recent study of an algal-based stream food web found that experimental warming increased the biomass of larger-bodied taxa, but the general response of invertebrate communities, including in detritus-based ecosystems, remains unknown. The Metabolic Theory of Ecology predicts that energetic demand will increase with temperature, reducing total abundance and biomass of organisms. Alternatively, responses to warming could be dominated by shifts towards taxa that differ both in body size and thermal preference, making community turnover more important in structuring post-warming communities. We tested the effects of higher temperatures in two headwater forest streams (one reference, one experimentally warmed by 2.3°C) in North Carolina, USA, by quantifying invertebrate structure monthly over 3.5 years (one pre-treatment year followed by 2.5 years of warming). Warming did not have a significant effect on mean annual biomass, abundance, or community structure. However, a size-structure shift was observed, with large-bodied taxa (Lanthus, oligochaetes, Cordulegaster, and Pycnopsyche) responding negatively to warming relative to smaller-bodied taxa (chironomid and ceratopogonid midges). Our results suggest that warming reassembles detritus-based communities within the fixed energetic constraints imposed by allochthonous inputs via community turnover of species that differ in body size. Changes in stream community size-structure due to warming could reduce the stability of forest stream food webs and alter their role in controlling carbon flow through stream ecosystems.