To study fisheries impact at the species level in temperate sandy bottom areas, a controlled field manipulation experiment was designed focusing on areas with high densities of the habitat-structuring, tube-dwelling polychaete Lanice conchilega (i.e. L. conchilega reefs). The hypothesis was that the impact on L. conchilega would be minimal, but that the fauna benefiting from the biogenically structured habitat would be impacted by beam-trawling. In this study, the impact of beam-trawl passage on intertidal L. conchilega reefs and its associated fauna was quantified. A treatment zone was exposed to a one-off experimental trawling. Subsequently, the impact on and recovery of the associated fauna was investigated for a period of 9 days post-impact. Community analysis showed a clear impact followed by a relatively quick recovery as apparent through MDS analysis (stress 0.06), a significant (p < 0.001) IMS of 0.61, through ANOSIM analysis: significant (p = 0.001) dissimilarities between treatment and control and through SIMPER analysis (decreasing dissimilarities over time). This impact and subsequent recovery was largely explained by two species: Eumida sanguinea and Urothoe poseidonis. Species analysis confirmed the beam-trawl passage significantly (p = 0.001) impacted E. sanguinea for the whole period of the experiment. The experiment confirmed that closely associated species of L. conchilega reefs are impacted by beam-trawl fisheries. This small-scale intertidal study provides some pointers which indicate that the tightly associated species will be impacted significantly when beam-trawling L. conchilega reefs in subtidal areas.