The mycorrhizal fungi are symbiotic organisms able to provide many benefits to crop production by supplying a set of ecosystem functions. A recent ecological approach based on the ability of the fungi community to influence plant-plant interactions by extraradical mycelium development may be applied to diversified, herbaceous agroecosystems. Our hypothesis is that the introduction of a winter cereal cover crop (CC) as arbuscular mycorrhizal fungi (AMF)-host plant in an organic rotation can boosts the AMF colonization of the other plants, influencing crop-weed interference. In a 4-years organic rotation, the effect of two winter cereal CC, rye and spelt, on weed density and AMF colonization was evaluated. The AMF extraradical mycelium on CC and weeds roots was observed by scanning electron microscopy analysis. By joining data of plant density and mycorrhization, we built the mycorrhizal colonization intensity of the Agroecosystem indicator (MA%). Both the CC were colonized by soil AMF, being the mycorrhizal colonization intensity (%) affected by environmental conditions. Under CC, the weed density was reduced, due to the increase of the reciprocal competition in favor of CC, which benefited from mycorrhizal colonization and promoted the development of AMF extraradical mycelium. Even though non-host plants, some weed species showed an increased mycorrhizal colonization in presence of CC respect to the control. Under intense rainfall, the MA% was less sensitive to the CC introduction. On the opposite, under highly competitive conditions, both the CC boosted significantly the mycorrhization of coexistent plants in the agroecosystem. The proposed indicator measured the agroecological service provided by the considered CCs in promoting or inhibiting the overall AMF colonization of the studied agroecosystems, as affected by weed selection and growth: It informs about agroecosystem resilience and may be profitably applied to indicate the extent of the linkage of specific crop traits to agroecosystem services, contributing to further develop the functional biodiversity theory.