Facilities for the production of microalgal biomass often suffer large losses in productivity as a result of biological contamination of cultures by ciliates, unicellular protozoans that feed on microalgae. Garlic oil is a low-cost natural product that is known to be active against several protozoans. In this study, we investigated whether garlic oil can be used to control ciliate contamination in microalgal cultures, using the ciliate Oxytricha and the microalga Chlamydomonas as a model system. Low doses of garlic oil (5–10 mg L−1) were capable of eradicating the ciliate Oxytricha from a contaminated Chlamydomonas culture within 1 day without influencing the productivity of the Chlamydomonas culture. The LD50 of garlic oil to the ciliate (3 mg L−1) was 19 times lower than the LD50 to the microalgae, which implies a low risk to the microalgal culture in case of overdosing. Analysis of the garlic oil indicated that it was composed mainly of polysulfides, with the main compound being diallyl disulfide. Diallyl disulfide had a lower toxicity to the ciliate (LD50 14 mg L−1) than garlic oil, indicating that diallyl disulfide is not the main active compound in garlic oil against the ciliate. Because garlic oil has a low cost, is already approved for use in agri- and aquacultures, has a low toxicity to humans, and is biodegradable, it may offer a sustainable solution to control biological contamination by ciliates in microalgal cultures.