Abstract The abundant amphipod Corophium volutator is an ecosystem engineer in soft-bottom intertidal communities due to its grazing and bioturbation activity. However, the amphipod commonly serves as second intermediate host for detrimental microphallid trematodes. This host–parasite association is potentially very sensitive to climate change as the transmission rate of larval trematodes (cercariae) from first intermediate hosts (mud snails) to amphipods, and hence infection intensity-dependent amphipod mortality, generally accelerates with increasing temperature. Given the ecosystem engineering role of C. volutator, we hypothesized that elevated temperature, indirectly through increased parasite-induced amphipod mortality, significantly affects the structure of the surrounding benthic community. To test this, we performed a three-month outdoor mesocosm experiment exposing a natural soft-bottom community of benthic plants and animals to four different treatments: relatively low mean water temperature (18°C) with low (<4%) and high (c. 31%) trematode prevalence in the snail population, and relatively high mean water temperature (22°C) with low and high trematode prevalence. Both temperature and snail parasitism had a significant impact on amphipod abundance and resulted in their almost complete eradication at the warm temperature with high parasitism. Aside from the amphipod hosts, increased temperature affected the abundance of eight faunal species out of 22 in total (36%), whereas increased level of parasitism or the parasite–temperature interaction influenced the density of three species (14%). The treatment-determined Corophium abundance played an isolated role for several species, particularly the polychaetes Hediste diversicolor (positive) and Polydora ligni (negative). Regarding primary producers, the overall frequency distribution of 21 species of benthic diatoms differed between all four treatments. Species-specific effects were few and weak, however, and microalgal abundance (chlorophyll-a) was statistically unaffected by treatments, together suggesting a rather resilient plant community towards the experimental perturbations. At the community level, the non-host macrofaunal diversity decreased with temperature in the low parasitism treatments whereas it increased with temperature in the high parasitism treatments. This suggests that sufficiently high levels of parasitism may turn a negative effect of elevated temperature on macrofaunal biodiversity into a positive effect. Hence, our experiment demonstrates that the synergy between parasitism and a relevant temperature increase, e.g. in lieu of climate oscillations or global warming, may have broad ecological consequences for the organization and function of soft-bottom communities, in part through elevated parasite-induced mortality of a central community member.