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Blastocystis, a common protist in the human gut microbiota, has been identified as a key modulator of gut health and disease progression. Research highlights the involvement of Blastocystis in inflammatory bowel disease, cognitive function, and metabolic health. Despite an increasing interest on this topic, the literature on Blastocystis remains fragmented and often contradictory, with subtype-specific effects inadequately defined and their underlying mechanisms insufficiently elucidated. In this Personal View, we provide an in-depth discussion of the dual roles of Blastocystis subtypes that can either exacerbate gut inflammation by disrupting the epithelial barrier or confer protection by enhancing barrier integrity and inducing anti-inflammatory immune responses. We also examine the effect of Blastocystis on the gut-brain axis, identifying associations between Blastocystis colonisation and cognitive and behavioural changes mediated through alterations in gut microbial composition and metabolite profiles. Moreover, we highlight the association of Blastocystis colonisation with healthier dietary patterns and improved cardiometabolic profiles. These findings could contribute to a comprehensive understanding of Blastocystis and its potential as a biomarker of gut health.