Intraspecific phenotypic variation is a significant component of biodiversity. Body size, for example, is variable and critical for structuring communities. We need to understand how homogenous and variably-sized populations differ in their ecological responses or effects if we are to have a robust understanding of communities. We manipulated body size variation in consumer (tadpole) populations in mesocosms (both with and without predators), keeping mean size and density of these consumers constant. Size-variable consumer populations exhibited stronger antipredator responses (reduced activity), which had a cascading effect of increasing the biomass of the consumer’s resources. Predators foraged less when consumers were variable in size, and this may have mediated the differential effects of predators on the community composition of alternative prey (zooplankton). All trophic levels responded to differences in consumer size variation, demonstrating that intrapopulation phenotypic variability can significantly alter interspecific ecological interactions. Furthermore, we identify a key mechanism (size thresholds for predation risk) that may mediate impacts of size variation in natural communities. Together, our results suggest that phenotypic variability plays a significant role in structuring ecological communities.