Cryptic belowground organisms are difficult to observe and their responses to global changes are not well understood. Nevertheless, there is reason to believe that interactions among above- and belowground communities may mediate ecosystem responses to global change. We used grassland mesocosms to manipulate the abundance of one important group of soil organisms, arbuscular mycorrhizal (AM) fungi, and to study community and ecosystem responses to CO2 and N enrichment. Responses of plants, AM fungi, phospholipid fatty acids and community-level physiological profiles were measured after two growing seasons. Ecosystem responses were examined by measuring net primary production (NPP), evapotranspiration, total soil organic matter (SOM), and extractable mineral N. Structural equation modeling was used to examine the causal relationships among treatments and response variables. We found that while CO2 and N tended to directly impact ecosystem functions (evapotranspiration and NPP, respectively), AM fungi indirectly impacted ecosystem functions by influencing the community composition of plants and other root fungi, soil fungi and soil bacteria. We found that the mycotrophic status of the dominant plant species in the mesocosms determined whether the presence of AM fungi increased or decreased NPP. Mycotrophic grasses dominated the mesocosm communities during the first growing season, and the mycorrhizal treatments had the highest NPP. In contrast, nonmycotrophic forbs were dominant during the second growing season and the mycorrhizal treatments had the lowest NPP. The composition of the plant community strongly influenced soil N, and the community composition of soil organisms strongly influenced SOM accumulation in the mesocosms. These results show how linkages between above- and belowground communities can determine ecosystem responses to global change.