Plants and soils are a critically important element in the global carbon-energy equation. It is estimated that in forest ecosystems over two-thirds of the carbon is contained in soils and peat deposits. Despite the importance of forest soils in the global carbon cycle, fluxes of carbon associated with fundamental processes and soil functional groups are inadequately quantified, limiting our understanding of carbon movement and sequestration in soils. The authors report the direct measurement of carbon in and through all major pools of a mycorrhizal (fungus-root) coniferous seedling (a complete carbon budget). The mycorrhizal symbiont reduces overall retention of carbon in the plant-fungus symbiosis by increasing carbon in roots and below-ground respiration and reducing its retention and release above ground. Below ground, mycorrhizal plants shifted allocation of carbon to pools that are rapidly turned over, primarily to fine roots and fungal hyphae, the host root and fungal respiration. Mycorrhizae alter the size of below-ground carbon pools, the quality and, therefore, the retention time of carbon below ground.