Proteins, peptides and amino acids (AA) that bypass upper gastrointestinal (GI) digestion can be fermented in the colonic regions. This could lead to prebiotic effects leading to enhanced production of health promoting short chain fatty acid (SCFAs). Alternatively, such nitrogenous compounds can be fermented to generate potentially harmful branched chain fatty acid (BCFAs). As collagen hydrolysates (CH), a nutraceutical that is clinically proven to control osteoarthritic pain, contain a high peptide content, a study was performed to evaluate whether peptides generated from intestinal digestion of CHs leads to microbial production of SCFAs and BCFAs. The CHs were subjected to digestive enzymatic processes and microbial fermentation in a dynamic computer-controlled GI model containing human fecal matter with samples taken at 0, 8, 16 and 24 h. In the ascending colonic vessel after 24 h, CH-OPT showed a significant (p<0.05) increase in SCFAs (propionic, butyric and valeric acids) with no changes observed in this reactor with CH-GL. Likewise, only CH-OPT showed a significant (p<0.05) increase in BCFAs (isovaleric and isobutyric acids) after 24 h in the ascending and transverse colonic reactors respectively. A significant (p<0.05) increase in heptanoic acid was observed at 24 h in the transverse colon for both CHs. The present study findings demonstrate that CHs can impact the microbial production of SCFAs and BCFAs. More studies are needed to determine the physiological significance of these microbial metabolites from intake of different formulations, higher doses of peptide CH supplements, and on the microbiome from various osteoarthritic stages.