Rising atmospheric carbon dioxide partial pressure (pCO2) and nitrogen (N) deposition are important components of global environmental change. In the Swiss free air carbon dioxide enrichment (FACE) experiment, the effect of altered atmospheric pCO2 (35 vs. 60 Pa) and the influence of two different N-fertilization regimes (14 vs. 56 g N m−2 a−1) on root colonization by arbuscular mycorrhizal fungi (AMF) and other fungi (non-AMF) of Lolium perenne and Trifolium repens were studied. Plants were grown in permanent monoculture plots, and fumigated during the growth period for 7 years. At elevated pCO2 AMF and non-AMF root colonization was generally increased in both plant species, with significant effects on colonization intensity and on hyphal and non-AMF colonization. The CO2 effect on arbuscules was marginally significant (P=0.076). Moreover, the number of small AMF spores (≤100 μm) in the soils of monocultures (at low-N fertilization) of both plant species was significantly increased, whereas that of large spores (>100 μm) was increased only in L. perenne plots. N fertilization resulted in a significant decrease of root colonization in L. perenne, including the AMF parameters, hyphae, arbuscules, vesicles and intensity, but not in T. repens. This phenomenon was probably caused by different C-sink limitations of grass and legume. Lacking effects of CO2 fumigation on intraradical AMF structures (under high-N fertilization) and no response to N fertilization of arbuscules, vesicles and colonization intensity suggest that the function of AMF in T. repens was non-nutritional. In L. perenne, however, AM symbiosis may have amended N nutrition, because all root colonization parameters were significantly increased under low-N fertilization, whereas under high-N fertilization only vesicle colonization was increased. Commonly observed P-nutritional benefits from AMF appeared to be absent under the phosphorus-rich soil conditions of our field experiment. We hypothesize that in well-fertilized agricultural ecosystems, grasses benefit from improved N nutrition and legumes benefit from increased protection against pathogens and/or herbivores. This is different from what is expected in nutritionally limited plant communities.