Although high-protein diets are widespread, the fate of dietary protein, its fermentation by gut microbiota, and the resulting effects on intestinal health are not yet fully understood. This article provides a comprehensive overview of microbial protein fermentation and its impact on intestinal health. We focus on the bacterial anabolic and catabolic pathways involved in microbial protein metabolism and the generation of metabolites such as ammonia, biogenic amines (BAs), and short-chain fatty acids (SCFAs). This review also examines how excessive dietary protein affects intestinal health. Elevated protein levels may disrupt microbial homeostasis, promoting the proliferation of pathogenic bacteria while reducing beneficial microbiota. Furthermore, enhanced bacterial metabolic activity can lead to greater production of harmful compounds such as BAs. These alterations are associated with impaired intestinal barrier function, immune dysregulation, and elevated inflammatory responses. Further research is necessary to clarify the metabolism of high-protein diets and their consequences for intestinal health.