Abstract Mounting evidence suggests that the transmission of certain parasites is facilitated by increasing temperatures, causing their host population to decline. However, no study has yet addressed how temperature and parasitism may combine to shape the functional structure of a whole host community in the face of global warming. Here, we apply an outdoor mesocosm approach supported by field surveys to elucidate this question in a diverse intertidal community of amphipods infected by the pathogenic microphallid trematode, Maritrema novaezealandensis. Under present temperature (17°C) and level of parasitism, the parasite had little impact on the host community. However, elevating the temperature to 21°C in presence of parasites induced massive structural changes: amphipod abundances decreased species‐specifically, affecting epibenthic species but leaving infaunal species largely untouched. In effect, species diversity dropped significantly. In contrast, 4‐degree higher temperatures in absence of parasitism had limited influence on the amphipod community. Further elevating temperatures (19‐26°C) and parasitism, simulating a prolonged heat‐wave scenario, resulted in an almost complete parasite‐induced extermination of the amphipod community at 26°C. In addition, at 19°C, just two degrees above the present average, a similar temperature‐parasite synergistic impact on community structure emerged as seen at 21°C under lower parasite pressure. The heat‐wave temperature of 26°C per se affected the amphipod community in a comparable way: species diversity declined and the infaunal species were favoured at the expense of epibenthic species. Our experimental findings are corroborated by field data demonstrating a strong negative relationship between current amphipod species richness and the level of Maritrema parasitism across 12 sites. Hence, owing to the synergistic impact of temperature and parasitism, our study predicts that coastal amphipod communities will deteriorate in terms of abundance and diversity in face of anticipated global warming, functionally changing them to be dominated by infaunal species. This article is protected by copyright. All rights reserved.