The resource base of aquatic food webs is changing due to land use and climate change, resulting in proliferation of algae and reductions in detrital carbon (C) that serve as both food and habitat for organisms. To inform predictions about how warming affects C cycling in headwater streams, we constructed C budgets for an experimentally warmed (EXP) and a reference (REF) stream. Our study took place in deciduous forest headwaters with high annual inputs of terrestrial organic matter and robust populations of microorganisms and detritivores. We quantified respiration rates on fine and coarse particulate organic matter (FPOM, CPOM [leaves and wood]) and measured inputs, standing stocks, and exports of various forms of C. We achieved a 2.3ºC mean increase in temperature in the EXP vs REF stream over the 34-months of experimental warming. Warming reduced C storage and increased C export, primarily as FPOM. Respiration rates on leaves, FPOM, and wood all increased with warming, with increases similar to predictions from metabolic theory. Areal respiration rates increased 1.2x and standing stocks of both CPOM and FPOM were reduced in the EXP vs REF stream (0.8x and 0.9x, respectively); however, neither increases in substrate-specific respiration nor reductions in standing stocks were statistically significant. Export of FPOM increased 1.4x in the EXP stream relative to the REF stream (P = 0.02). These patterns are consistent with predictions that warming stimulates metabolism of microorganisms and detritivores, increasing processing rates and lowering C storage. A concurrent litter breakdown study showed that detritivore-mediated C processing increased with warming to a greater extent than microbial processing. The relatively large C loss we observed with a moderate amount of warming indicates that detrital resources need protection and conservation given current and predicted increases in stream temperature.