The use of blue mussel farming in the Baltic Sea for mitigating eutrophication through nutrient bioextraction has recently been under debate, with emphasis on potential local negative effects induced by farmed mussels, based on theoretical scenarios. Here, we broaden the discussion by presenting an assessment of the faunal community around a non-commercial mussel farm, after two years of operation in a relatively well-oxygenated water area. It is the first large-sized farm (25 tons) in the northern Baltic proper. The biotic conditions at this mussel farm did not deviate negatively from surrounding reference areas. Total abundance and species richness of sediment-dwelling fauna were higher at the farm site, which also showed a distinct zoobenthic species composition including many bioturbators which may provide extra protection against hypoxia. A snap-shot view of water quality indicated relatively low P- and chlorophyll-a concentrations at the farm. We caution against drawing conclusions from our study that are too far-reaching primarily, due to the mussel farm in question being smaller than those referred to in the debate. However, the study presents an important initial assessment of the functioning of a pilot mussel farm in the Baltic proper and provides baselines for future investigations and guidelines for improved sampling design.