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In experimental metacommunities with marine benthic microalgae, we tested whether heat stress changes effects of connectivity and habitat heterogeneity on metacommunity structure and functioning, by manipulating a simulated heat wave, dispersal frequency and a light intensity gradient. We found that all measures of mean local and regional diversity and community biomass significantly declined after the heat wave and showed no sign of recovery. Additionally, dispersal decreased diversity and increased dominance in both the heat stressed and control communities. Together the heat wave and high dispersal frequency induced a dominance shift by spreading a temperature tolerant but low yielding species from its source patches with low light intensity across the metacommunity, an effect that increased with time. Although different species became dominant at high dispersal frequency with and without the heat wave, the shift towards a temperature tolerant species was not sufficient to maintain total community biomass. Thus, short-term disturbance may cause longer-term loss of ecosystem function due to dominance shifts in the composition of communities. This study illustrates the importance of employing multispecies approaches when attempting to predict responses of communities to environmental changes.