Species that modify their surroundings are known as ecosystem engineers. For example, patches of polychaete tubes enhance soft-bottom intertidal habitat complexity, modifying water flow, promoting sediment accretion and affecting nutrient fluxes at the water–sediment interface. Understanding how such structures affect the benthic ecosystem’s functioning requires the assessment of their influence on all benthic components and how the related ecosystem services may be modified. We performed an in situ experimental study, involving the use of artificial mimics of polychaete tubes, to investigate the purely physical impacts of the structures without the complexity of worm activity. Benthic chambers of different mimic densities were used, and their effect on the recolonisation of defaunated natural sandy sediments by microorganisms, meiofauna and macrofauna was monitored. We also measured air–sediment CO2 fluxes and sediment stability as they constitute crucial ecosystem services provided by benthic habitats. We showed that the biogenic structures stimulated the development of diatom biofilms (microphytobenthos) and their associated extracellular polymeric substances (EPS). Impacts of tubes on meiofaunal and macrofaunal assemblages were significant; in most cases, species and groups were more abundant in treatments with few or no tubes. In response to the tube density increase, the whole system tended towards heterotrophy and higher sediment stability, probably as a consequence of the development of the diatom biofilm. Biogenic structures are, therefore, of critical importance for soft-bottom intertidal communities in terms of both structure and function.