Zymoseptoria tritici, the causal agent of the foliar disease Septoria tritici blotch (STB), is a major wheat pathogen in Europe. Although several wheat resistance (R) genes have been identified, Z. tritici often evades recognition and continues to cause disease in the field. For example, the Stb6 R gene recognises the effector AvrStb6, yet the pathogen persists through field isolates expressing non-recognised but still highly expressed AvrStb6 isoforms. The consistent high expression of AvrStb6 during the biotrophic phase, and the lack of gene loss despite strong Stb6 selection pressure, suggest an important but unknown role during infection. Amplicon sequencing of apoplastic fluids from wheat infected with wild-type or ∆AvrStb6 mutants revealed significant shifts in the bacterial microbiome in the presence of AvrStb6. Similarly, 16S rRNA profiling identified Pseudomonas as the main genus affected by AvrStb6 presence or absence. In vitro confrontation assays confirmed that AvrStb6 influences interactions between Z. tritici and Pseudomonas spp. isolated from the wheat apoplast. Although the mode of action remains unclear, AlphaFold3-based structural predictions indicate that AvrStb6 has two distinct positively charged regions that may interact with phosphatidyl groups on bacterial outer membranes. Ongoing protein and biochemistry work aims to elucidate how AvrStb6 modulates microbial dynamics within the wheat apoplast.