Stable carbon and nitrogen isotopic composition (δ13C and δ15N) of benthic organisms was investigated to understand the effects of a gregarious tubicolous amphipod species (Haploops nirae) on benthic food web structures and test whether drastic changes in species composition cause changes in food web structure. The habitat engineered by this species was sampled and compared with the adjacent uncolonized Amphiura filiformis muddy habitat in winter and summer. The isotopic signatures of macrofaunal and megafaunal species associated with both habitats were analysed along with potential food sources at each sampling period. Similar food web structures for each habitat (and each season), with high δ15N ranges spanning over 3 trophic levels, were reported although omnivory was less frequent in the H. nirae habitat. The amphipod H. nirae appears to play a baseline role, with the lowest δ15N values and δ13C values indicating that it primarily feeds on phytoplankton. Bayesian mixing models were used to estimate the contributions of potential food sources to the diet of the species accounting for most of the biomass in each habitat and showed that the epibionts covering tube mats are a key contribution to the food webs of both habitats. Identified as benthic diatoms, they may minimize interspecific food competition between dominant suspension feeders such as Polititapes virgineus or H. nirae within a habitat. This finding highlights the contribution of microphytobenthic producers to subtidal (~30 m deep) muddy habitat food webs, suggesting that the mucopolysaccharides composing the H. nirae tubes support the growth of a heterotrophic diatom population. As an engineer species, H. nirae acts as a facilitator for diatoms which ultimately sustain the secondary production of the H. nirae habitat as well as the immediate surrounding habitats.