The fungal pathogen Zymoseptoria tritici is the causal agent of Septoria tritici blotch (STB), a major wheat disease in Western Europe. Microorganisms inhabiting wheat leaves might act as beneficial, biocontrol or facilitating agents that could limit or stimulate the development of Z. tritici. Improving our understanding of microbial communities in the wheat phyllosphere would lead to new insights into STB management. The current resource announcement details the fungal and bacterial metabarcoding datasets obtained by sampling wheat leaves infected by Z. tritici. Tissues with different symptomatology were sampled from three wheat commercial varieties on different sampling dates during a cropping season. Weeds around wheat fields were sampled as complements to the wheat datasets. In total, more than 450 samples were collected. The presence of the pathogen Z. tritici was also quantified using qPCR. We provide the raw metabarcoding datasets, the Amplicon Sequence Variant (ASV) tables obtained after bioinformatic processing, the metadata describing sampling dates, wheat varieties and tissue health condition, a preliminary descriptive analysis of the data, and the code used for bioinformatic and descriptive statistical analysis.