Proanthocyanidins (PACs) are the bioactive components naturally present in daily diet, especially in fruits and vegetables. Multiple pieces of evidence suggested that ingestion of PACs or diets full of PACs might contribute to physiological benefits, such as metabolic syndrome regulation, immune modulation, cancer prevention, and neuroprotection. Many studies stated that dysbiosis is closely linked with the abovementioned health conditions, and the extremely poor bioavailability of PACs, directly associated with the structural diversity, leads to extensively metabolized through gut microbiota (GM). GM transforms PACs into bioactive metabolites. Conversely, PACs also modulate the gut microbiome and the composition of GM. Thus, the complex bidirectional interactions between PACs and gut microbiota might help to understand the ambiguity between bioavailability and pleiotropic bioactivity. In this review, we summarize recent in vivo and in vitro studies from the aspect of intestinal function of PACs and its associated disease, as well as the underlying mechanisms.