Habitat modifying organisms can alter the distribution of associated species. We surveyed soft-sediment patches in Bodega Harbor, California and found that patches with high densities of the phoronid Phoronopsis harmeri (Pixell, 1912), a chemically-defended tube-building lophophorate, have higher infaunal abundance and richness than similar patches with low densities of P. harmeri. To determine whether this difference was driven by P. harmeri and whether this difference is attributable to the activities of the organism, or simply its physical structure, we conducted a field experiment with four treatments: live phoronids, mimics of phoronid structure, phoronid-free sediments (bare) and unmanipulated sediments. Although the field experiment did not detect differences in the overall abundance or richness of infauna among the manipulated treatments, some of the individual species did show a positive response to the presence of phoronids and phoronid structure (i.e., mimics). In particular, the polychaete Boccardia proboscidea, the amphipod Monocorophium uenoi, and harpacticoid copepods were facilitated by the presence of phoronids and phoronid structure when there was sediment disturbance. The inconsistency between the results of the survey and of the manipulative experiment may be largely driven by the disturbance caused by the manipulation. However, where P. harmeri has an effect, it is generally positively associated with infaunal abundance that may be attributable to the stabilization of sediments.