The role of intestinal microflora in digestive and metabolic processes has received increasing attention from researchers and clinicians. Both enterocytes and small intestine luminal microorganisms can degrade peptides and amino acids (AA). Further, enterocytes can utilize ammonia via glutamate, glutamine, citrulline, and urea synthesis, whereas luminal microbes will deaminate AA, hydrolyze luminal urea, and recycle this ammonia by synthesis of new microbial cells. Although, undoubtedly, some indispensable AA may arise from N cycling and microbial synthesis in the intestinal lumen, the actual net impact on protein nutrition status appears to be limited in humans and animals. Moreover, potential contributions of the recycled N as colonic luminal microbial proteins to AA in blood depend on colonic protein digestion and AA absorption. Finally, new evidence indicates that gut microbial metabolism may be enhanced by prebiotics and probiotics, with the prospects of new treatment paradigms for eliminating undesirable secondary N metabolites and ameliorating complications in whole-body N metabolism under the conditions of intestinal stress, liver disease, and kidney failure.