Ecosystem engineering is a ubiquitous process by which the biological activity of a species shapes habitat diversity and often creates local biodiversity hotspots. The honeycomb-worm Sabellaria alveolata, an intertidal ecosystem engineer, actively builds reefs across Europe by aggregating sand. Here, we used carbon and nitrogen isotopic compositions measured on basal resources and bentho-demersal consumers (fish, mega- and macroinvertebrates) to empirically investigate how non-trophic interactions (ecosystem engineering) modify food web structure and functioning. Three sediment types corresponding to different substrata and species assemblages were sampled: a control soft sediment (medium to muddy sand, before the establishment of S. alveolata), the sediment engineered by S. alveolata (hardened 3D structures), and the soft sediment under the influence of S. alveolata (associated sediment). Using consumer community isotopic biplots (biomass-weighted), niche metrics (standard ellipse area), and mixing models, we found that S. alveolata, through the physical structure it creates, the stimulation of basal resources (microphytobenthos and Ulva), and the diversification of suspension-feeding species, promotes benthic-pelagic coupling and a habitat-wide form of 'gardening,' which further leads to trophic pathway diversification and limits trophic competition between the engineer species and associated suspension-feeders. Furthermore, our results help to refine the definition of S. alveolata reefs as the sum of the engineered and associated sediments since they are part of a single reef food web coupled by the stimulated basal resources and consumers. Finally, the non-trophic and trophic interactions mediated by S. alveolata and the associated macrofauna seem to promote the establishment of a temporally stable and probably highly resilient reef habitat.