Increasing species richness of primary producers or consumers is proposed to increase primary and secondary production; however, the consequences of biodiversity change across trophic levels has been poorly investigated. We used a controlled marine microbial system to investigate the effects of simultaneous changes in biodiversity of consumer and prey species. Consumer (ciliates) and prey (algae) richness and identity were manipulated independently in a complete factorial design. The results showed clear biodiversity effects of both consumers and prey, within and across trophic levels. We found reduced prey and increased consumer biomass with increased consumer richness, with the most diverse prey assemblage supporting the highest biomass of consumers at the highest richness of consumers. Increasing prey richness did not increase resistance to consumption when consumers were present. Instead, our results indicated enhanced energy transfer with simultaneous increasing richness of consumers and prey.