Agricultural intensification reduces not only biodiversity in agroecosystems but also key ecosystem functions such as soil fertility. By reintroducing biological diversity in fields, weeds may enhance soil biological fertility through their influence on crop microbiota. However, letting weeds grow in crop fields will depend on weed competitiveness, farmers' perception and acceptance, and on crop management, which influences the occurrence and the abundance of weeds in the field. This study assessed the use of eight weed species to modify wheat plant root endospheric mycobiota, and the applicability of using these plants for mycobiota enrichment in the field. By combining controlled lab experiments and field studies, we demonstrated that weeds act either as a refuge for a high diversity of fungi or as a vector for transferring fungi to the crop, particularly symbionts. Weeds differed in their competitive effect on wheat growth and only three species significantly reduced wheat growth. Interviews with farmers' revealed that weed species were better known and more appreciated in crop fields by organic farmers than by conventional farmers. Floristic surveys confirmed that both weed occurrence and cover were higher in organic fields than in conventional fields. A multicriteria analysis showed that Trifolium repens and V. persica had the highest potential for promoting wheat plant mycobiota. Among the weed species tested, these two are worth considering as auxiliaries to improve soil biological fertility in crop fields. Their use with the goal of selecting appropriate crop mycobiota should be relatively easier in organic farms where weeds are better accepted, whereas their use in conventional farms would require raising farmers' awareness of the benefits of weeds for soil fertility.