Natural products play a pivotal role in human health by exerting bioactive effects, including the modulation of the gut microbiome. Cacao, a widely consumed natural product, is rich in polyphenols and dietary fiber, which may influence microbial composition and metabolic functions. However, its effects on the gut microbiota remain poorly understood, particularly regarding inter-individual differences. This study investigated the impact of cacao on gut microbiota using an in vitro fecal incubation model with samples from healthy Korean adults. Our findings classified the gut microbiota of Korean individuals into two distinct enterotypes: and . In the enterotype, cacao treatment significantly increased the relative abundance of beneficial bacterial genera, including , , and . Conversely, in the enterotype, cacao treatment was associated with an increase in the relative abundance of ; however, the small sample size and community shifts during incubation limited the robustness of this observation. Functional predictions based on KEGG pathways further revealed enterotype-specific differences. In the enterotype, the cacao-treated group exhibited enhanced pathways associated with starch, sucrose, galactose, and thiamine metabolism, which was not observed in the enterotype. These findings suggest a potential role for cacao as a gut microbiome modulator, highlighting its possible utility in microbiome-targeted dietary interventions and therapeutic strategies.