Estuarine and coastal mudflats are some of the most diverse and productive ecosystems, underpinning ecosystem services such as fishing, aquaculture, and coastal protection. Microphytobenthos (MPB) are the main primary producers in these soft-sediment intertidal habitats, but their top-down and bottom-up interactions with invertebrates are poorly understood. Using a manipulative field experiment, I investigated how the deposit feeder, Pyrazus ebeninus, the grazer Bembicum auratum and the predator, Conuber sordidus independently and interactively influence the biomass and assemblage composition of MPB at a time scale of 2 days, and how P. ebeninus influences MPB and co-occurring invertebrates at time scales up to 3 months. At 2 days, MPB biomass was reduced in plots with Pyrazus alone versus control plots (without macrofauna), or versus plots where Bembicium was also present. By 21 days, however, the pattern had reversed with more MPB in plots with Pyrazus and by 3 months there was no significant difference. Temporally variable effects of macrofauna on community composition were also seen. The results highlight the complex interplay between MPB and macrofauna across temporal and spatial scales, and the need to understand these to build robust estuarine management strategies.