The seasonal dynamics of a community of endomycorrhizal fungal morphotypes in the roots of three grassland species (Achillea millefolium, Poa angustifolia, Plantago lanceolata) was evaluated, together with the effects of experimental treatment (mowing and phosphorus application) and the host plant properties. Strong seasonal variability was found in the fungal community, where clear seasonal patterns can be distinguished for several fungal morphotypes. The sampling date explained 20 to 30% of the total compositional variability for all three host species. The Plantago roots host the highest number of arbuscular mycorrhizal (AM) fungal populations. There are two co-dominant fungal morphotypes in Achillea roots (assigned to the genera Scutellospora and Glomus) and only one strongly dominant morphotype (assigned to Glomus), in the Poa roots, All three host species have a comparable pattern of richness of AM morphotypes with a single peak in the summer, possibly aligned with the flowering time of the host. This study found only a limited effect of mowing (on the abundance of Scutellospora-like morphotypes in the Poa roots) and no effect of fertilization with phosphorus. The effect of developmental age of individual host plants on the composition of the endomycorrhizal community was found in Plantago, but not in Achillea or Poa.