Despite free-living protozoa being a major factor in modifying aquatic autotrophic biomass, ciliate−cyanobacteria interactions and their functional ecological roles have been poorly described, especially with toxic cyanobacteria. Trophic relationships have been neglected and grazing experiments give contradictory evidence when toxic taxa such as Microcystis are involved. Here, 2 toxic Microcystis strains (containing microcystins), 1 non-toxic Microcystis strain and a non-toxic green alga, Chlorella vulgaris, were used to investigate predator−prey interactions with a phagotrophic ciliate, Blepharisma americanum. Flow cytometric analysis for microalgal measurements and a rapid ultra high performance liquid chromatography-tandem mass spectrometry protocol to quantify microcystins showed that non-toxic photosynthetic microbes were significantly grazed by B. americanum, which sustained ciliate populations. In contrast, despite constant ingestion of toxic Microcystis, rapid egestion of cells occurred. The lack of digestion resulted in no significant control of toxic cyanobacteria densities, a complete reduction in ciliate numbers, and no observable encystment or cannibalistic behaviour (gigantism). Individual B. americanum morphological responses (biovolume and cell width) showed a significant decrease over time when sustained on non-toxic Microcystis compared to grazed C. vulgaris populations, supporting previous studies that cyanobacteria may be a relatively poor source of nutrition. Results here provide insight into the ecological interactions of ciliates and cyanobacteria, and for the first time B. americanum is shown to have the capacity to suppress potentially bloom-forming cyanobacteria. However, grazing can be significantly altered by the presence of microcystins, which could have an impact on bloom dynamics and overall community structure.