Phenotypic trait differences between species are expected to play an essential role in community assembly. However, the magnitude of trait variability between individuals of the same species is increasingly recognized to have significant ecological effects, including maintaining species diversity. Here we ask how within-species trait diversity at the consumer trophic level affects consumer competition and prey community dynamics at lower trophic levels in an experimental microbial ecosystem consisting of ciliated protozoa, nematode worms, and bacterial prey. Although the nematode had an inherent competitive advantage and rapidly excluded ciliates with low trait variance, we found that high trait variance in the ciliate inverted the consumer hierarchy, ultimately excluding the nematode. Competition between the high trait variance ciliate and the nematode altered the temporal trajectories of individual prey species in non-additive ways, mediated by prey traits related to growth rate and defense. We performed pairwise co-cultures with each consumer and prey species and found that high trait variance in the ciliate increased the mean prey consumption rate over the low trait variance ciliate, which led to an increase in selective feeding in the presence of all prey species. Overall, our results are consistent with predictions from the coexistence theory framework and are compelling evidence that intraspecific trait diversity in consumer species 1) modulates competitive differences between species at higher trophic levels and 2) generates cascading effects on the community composition at lower trophic levels.