Habitat engineers make strong and far-reaching imprints on ecosystem processes. In intertidal mudflats, the dominant primary producer, microphytobenthos (MPB), often forms high biomass patches around oyster reefs. We evaluate multiple hypotheses linking MPB with oyster reefs, including oyster biodeposition, meiofaunal grazing, and abiotic factors, aiming to help predict effects of reef removal or proliferation. We quantify spatial patterns of an Atlantic mudflat community and its environment around two large Crassostrea reefs before experimentally sacrificing one reef via burning. MPB biomass was enriched surrounding living oyster reefs although infaunal biomass and individual sizes were low. Structural equation modelling best supported the hypothesis that crab predation intensity, which decayed with distance from the reefs, locally freed MPB from grazing. Our results suggest that Crassostrea reef expansion may enrich local MPB patches and redirect trophic energy flows away from mudflat infauna, with potential implications for the sustainability of local fisheries and bird conservation.