Bioturbation processes influence particulate (sediment reworking) and dissolved (bioirrigation) fluxes at the sediment–water interface. Recent works showed that benthic foraminifera largely contribute to sediment reworking in intertidal mudflats, yet their role in bioirrigation processes remains unknown. In a laboratory experiment, we showed that foraminifera motion behaviour increased the oxygen penetration depth and decreased the total organic content. Their activity in the top 5 mm of the sediment also affected prokaryotic community structure. Indeed, in bioturbated sediment, bacterial richness was reduced, and sulfate-reducing taxa abundance in deeper layers was also reduced, probably inhibited by the larger oxygen penetration depth. Since foraminifera can modify both particulate and dissolved fluxes, their role as bioturbators can no longer be neglected. They are further able to mediate the prokaryotic community, suggesting that they play a major role in the benthic ecosystem functioning and may be the first described single-celled eukaryotic ecosystem engineers.