While parasitism is a common lifestyle on Earth, its importance for the functioning of marine ecosystems has been overlooked for a long time. In particular, parasites have significant potential to influence central ecological processes through their impacts on hosts that serve as ecosystem engineers. Using an ex situ experimental approach, we explored the effects of trematode parasites on the engineering bioturbation activity of a common and abundant bivalve along European Atlantic soft‐bottom coastlines, the peppery furrow shell Scrobicularia plana , as well as knock‐on effects for nutrient exchanges at the sediment–water interface (SWI). Trematodes negatively impacted the host's ability to transport sediment particles and solutes in a density‐dependent way, with parasite burden explaining 22–31% of the inter‐individual variability. This could be explained by parasitism impairing the bivalve physiological state and ability to burrow, as we observed a decrease in the condition index and the burrowing depth of the bivalves with an increase in the number of parasites they host. In contrast, the influence of S. plana on benthic biogeochemical fluxes did not vary significantly according to parasitic burden over a short time scale. Here, we focused on the effects of trematode parasites on the behaviour of S. plana alone, and thus excluded other macrofaunal organisms. We should next test whether trematodes modulate the structure and functioning of benthic communities dominated by S. plana to better understand and quantify the engineering role of parasites in soft‐bottom coastal environments.