The wheat pathogen Zymoseptoria tritici reproduces sexually during the intercropping season on crop residues, which act as primary inoculum source. Few studies have examined the impact of the whole microbial community on the saprophyte/sexual stage of such residue-borne pathogens. We characterized the interactions between Z. tritici and the micro-organisms present on residues and assessed the impact of some factors (soil contact, seasonality). To this end, residues of wheat plants preliminary inoculated with Z. tritici in greenhouse were left outdoor either with or without contact with soil. Non-inoculated residues were left in the same conditions, as control. Residue sampling was performed in July (before contact with ground), October, December and February. The experiment was repeated a second year. Following a metagenomic description of fungal and bacterial communities, linear discriminant analyses and ecological network analyses were combined to investigate how microbial communities were impacted by the infection. Foremost, we showed the influence of the infection, even after Z.tritici disappearance, on the structure and composition of the microbial communities of wheat residues. Interactions appeared to be mainly indirect, despite Z.tritici position in networks as key taxa. The presence of Z. tritici also impacted fungal and bacterial species previously reported as beneficial. Describing interactions within residues ecosystem may lead to new disease-management solutions.