An increase in tree mortality is currently evident in forests around the world. Such mortality could be counterbalanced by the native regeneration of seedlings. Seedling establishment under natural conditions is often limited by inter-plant competition and drought conditions. Many forest ecosystems rely on ectomycorrhizal relationships which could be affected by competition and drought, altering forest resilience. We carried out an experiment testing the combined effects of drought, herbaceous competition, and ectomycorrhizal fungi (EMF) on the growth and shape of Aleppo pine seedlings and the EMF community composition. Pines that germinated in the presence of the EMF spores were taller, had greater biomass, and more side branches. However, under conditions of either competition or drought, the effect of EMF on seedling biomass and height was greatly reduced, while the effect on shoot branching was maintained. Under a combination of drought and competition, EMF had no influence on plant growth and shape. The EMF community was strongly dominated by Geopora species, and its structure was not affected by the treatments. Plants experiencing competition were nitrogen poor but presented the highest levels of EMF sequence abundance. Stressful conditions seem to alter the relationship between EMF and seedling growth. Specifically, under drought, both colonization and seedling response to EMF was small. However, under competition, colonization was maintained while no growth enhancement was evident. This discrepancy highlights the complexity of the benefits provided to seedlings by EMF under ecologically relevant conditions.