Soil nutrients and light have major effects on the economics of arbuscular mycorrhizal (AM) symbioses. This study tests the main and interactive effects of soil fertility and light on AM fungal community. We conducted a 3 year mesocosm experiment with a full two factorial design: light (full light or shade) and soil fertility (unfertilized or fertilized), on the Qinghai-Tibetan Plateau. Plant traits, soil characteristics and the AM fungal communities inside roots and in soils were measured. Shade reduced AM colonization of roots, fertilization reduced the hyphal abundance in the soil, and both factors reduced species richness of AM fungi inside plant roots. Fertilization exacerbated the negative impacts of shade on AM fungal abundance and diversity. We observed 15 phylotypes of AM fungi inside roots and ten morphotypes of AM fungal spores in the soil. Taxa responded differently to shade and fertilization and there was little congruence between the responses of fungi inside the roots and in the spore community. Our findings indicate that both shade and fertilization reduce the abundance of AM fungi, but the two factors have different effects on the quality of plant roots as habitat for AM fungi.