Theory predicts that intraguild predation leads to different community dynamics than the trophic cascades of a linear food chain. However, experimental comparisons of these two food-web modules are rare. Mixotrophic plankton species combine photoautotrophic and heterotrophic nutrition by grazing upon other phytoplankton species. We found that the mixotrophic chrysophyte Ochromonas can grow autotrophically on ammonium, but not on nitrate. This offered a unique opportunity to compare predator–prey interactions in the presence and absence of intraguild predation, without changing the species composition of the community. With ammonium as nitrogen source, Ochromonas can compete with its autotrophic prey for nitrogen and therefore acts as intraguild predator. With nitrate, Ochromonas acts solely as predator, and is not in competition with its prey for nitrogen. We parameterized a simple intraguild predation model based on chemostat experiments with monocultures of Ochromonas and the toxic cyanobacterium Microcystis. Subsequently, we tested the model predictions by inoculating Ochromonas into the Microcystis monocultures, and vice versa. The results showed that Microcystis was a better competitor for ammonium than Ochromonas. In agreement with theoretical predictions, Microcystis was much more strongly suppressed by intraguild predation on ammonium than by top–down predation on nitrate. Yet, Microcystis persisted at very low population densities, because the type III functional response of Ochromonas implied that the grazing pressure upon Microcystis became low when Microcystis was rare. Our results provide experimental support for intraguild predation theory, and indicate that intraguild predation may enable biological control of microbial pest species.