While the effect of habitat connectivity on local and regional diversity has been analysed in a number of studies, time-dependent dynamics in metacommunities have received comparatively little consideration. When local patches of a metacommunity are identical in environmental conditions but differ in initial community composition, dispersal among patches may result in homogenization of local communities. In a microcosm experiment with benthic ciliates, we tested the hypothesis that the effect of connectivity on diversity is time-dependent and only transitory, with the degree of connectivity affecting the time to homogenization but not the final outcome. Six microcosms were connected to a metacommunity with one of three levels of connectivity. The six patches differed in initial community composition but were identical in environmental conditions. We found a time-dependent and transitory effect of connectivity on local and regional richness and on local Shannon diversity, while Bray-Curtis dissimilarity and regional Shannon diversity were persistently affected by connectivity. Local richness increased and regional richness decreased with connectivity during the initial phase of the experiment but soon converged to similar values in all three connectivity treatments. Local Shannon diversity was unimodally related to time, with maximum diversity reached sooner with high than with medium or low connectivity. Eventually, however, local diversity converged to similar values irrespective of connectivity. At the regional scale, Shannon diversity was persistently lower with high than with low connectivity. While initial differences in community composition vanished with medium and high connectivity, they were maintained with low connectivity resulting in persistently high beta and regional diversity. The effect of connectivity on ciliate community composition translated down to the algal resource, as stronger dominance of the superior competitor with high and medium connectivity resulted in stronger depletion of the resource.