AbstractIron flocculants play a major role in the remediation of water bodies, removing particulate pollutants such as microplastics through floc formation. Such flocs are prone to microbial iron reduction while lying on top of anoxic sediments, which possibly leads the release of bound microplastics. In this study, Shewanella oneidensis was employed to simulate the impact of microbial iron reduction on the release of polyethylene spheres from sunken flocs in 120 d batch experiments. Most of the flocs iron (oxyhydr)oxides were reduced (70–90%), but this did not affect their integrity. Only a negligible proportion (0.2–2.7%) of polyethylene spheres was released, while the majority remained bound inside the floc matrix. This study exemplifies that flocs are quite stable, even when experiencing microbial iron reduction under anoxic conditions. Thereby incorporation into such aggregates may display a potential mode of long‐term microplastics storage in freshwater sediments.