Five mesofauna communities varying in both structure and composition were exposed to phenanthrene in mesocosms for up to four months. Effects of phenanthrene were assessed on mesofauna population dynamics, fungal biomass (ergosterol concentrations), and litter decomposition (litter mass loss, nitrogen concentration). The effects of each community on the fate of phenanthrene were also assessed. We hypothesize that phenanthrene affects the population dynamics of mesofauna and soil biological functioning depending on exposure duration, type of community, or both. Results show that phenanthrene exerted an effect on mesofauna and that the effects on some species, like Folsomia fimetaria, were influenced by the species composition in the mesocosms, the soil layer, and the sampling date. However, the effects of phenanthrene on ergosterol content and organic matter decomposition were not significantly influenced by community composition. These results demonstrate that interspecific relationships are needed to assess the toxicity of pollutants and should be taken into account in ecotoxicological risk assessment. Furthermore, this work does not support the hypothesis of a direct link between toxic effects of organic pollutants on mesofauna species and soil biological functioning.