Avocado peel, a byproduct from the avocado pulp industry, is a promising source of polyphenolic compounds. We evaluated the effect of a proanthocyanidin-rich avocado peel polyphenol extract (AvPPE) on the composition and metabolic activity of human fecal microbiota cultured for 24 h in a bioreactor in the presence of high protein (HP) amounts and the effect of the resulting culture supernatants (CSs) on HT-29Glc-/+ and Caco-2 cells. AvPPE decreased the HP-induced production of ammonia, H2S, propionate, and isovalerate and increased that of indole and butyrate. Microbiota composition was marginally affected by HP, whileAvPPE increased the microorganisms/abundance of phylum Actinobacteria, families Coriobacteriaceae and Ruminococcaceae, and genus Faecalibacterium. AvPPE failed to prevent the HP-induced decrease of HT-29Glc-/+ cell viability and energy efficiency but prevented the HP-induced alterations of barrier function in Caco-2 cells. Additionally, the genotoxic effect of the CSs upon HT-29Glc-/+ was attenuated by AvPPE. Therefore, AvPPE may be considered as a promising product for improving colonic homeostasis.