PURPOSE: Blastocystis is one of the most prevalent intestinal protists detected in humans and animals worldwide, and its role in human health and disease has become an increasingly debated topic in parasitology. The study investigated the therapeutic potential of Allium tuncelianum extract, an endemic plant of Turkey, as an alternative treatment for Blastocystis ST3 infections. METHODS: The experimental animals were infected with Blastocystis ST3. The animals were divided into six groups: healthy control (G1), infected control (G2), infected Allium tuncelianum extract treatment (G3a, G3b, and G3c) and infected Metronidazole treatment (G4). Microscopic examination and qPCR methods were used to determine Blastocystis load in fecal samples. RESULTS: The G3c group (250 mg/kg/day Allium tuncelianum) complete (100.0%) microscopic clearance of Blastocystis load in fecal samples was achieved by day 12th, whereas the Metronidazole group (G4), showed only an 84.1% reduction. Moreover, qPCR results revealed lower Blastocystis loads in groups G3c and G3b compared to Metronidazole. A statistically significant decrease in fecal Blastocystis load was observed in all treated groups compared to the infected group (G2) (p < 0.0001). Blastocystis load in fecal sample reduction exhibited a dose-dependent pattern across all Allium tuncelianum treatment groups, confirming the dose-dependent therapeutic effect of the extract. Allium tuncelianum extract, especially at higher doses, may serve as a natural, effective, and safer alternative or supplement to Metronidazole in the management of Blastocystis infection. CONCLUSION: This study demonstrated that Allium tuncelianum extract exhibited superior therapeutic efficacy against Blastocystis ST3 compared to Metronidazole. The findings suggest that regular dietary consumption of Allium tuncelianum could represent a promising natural alternative for managing Blastocystis infections.