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Although fermentable carbohydrates (CHO) can reduce metabolites derived from dietary protein fermentation in the intestine of pigs, the interaction between site of fermentation and substrate availability along the gut is still unclear. The current study aimed at determining the impact of two different sources of carbohydrates in diets with low or very high protein content on microbial metabolite profiles along the gastrointestinal tract of piglets. Thirty-six piglets (n = 6 per group) were fed diets high (26%, HP) or low (18%, LP) in dietary protein and with or without two different sources of carbohydrates (12% sugar beet pulp, SBP, or 8% lignocellulose, LNC) in a 2 × 3 factorial design. After 3 weeks, contents from stomach, jejunum, ileum, caecum, proximal and distal colon were taken and analysed for major bacterial metabolites (D-lactate, L-lactate, short chain fatty acids, ammonia, amines, phenols and indols). Results indicate considerable fermentation of CHO and protein already in the stomach. HP diets increased the formation of ammonia, amines, phenolic and indolic compounds throughout the different parts of the intestine with most pronounced effects in the distal colon. Dietary SBP inclusion in LP diets favoured the formation of cadaverine in the proximal parts of the intestine. SBP mainly increased CHO-derived metabolites such as SCFA and lactate and decreased protein-derived metabolites in the large intestine. Based on metabolite profiles, LNC was partly fermented in the distal large intestine and reduced mainly phenols, indols and cadaverine, but not ammonia. Multivariate analysis confirmed more diet-specific metabolite patterns in the stomach, whereas the CHO addition was the main determinant in the caecum and proximal colon. The protein level mainly influenced the metabolite patterns in the distal colon. The results confirm the importance of CHO source to influence the formation of metabolites derived from protein fermentation along the intestinal tract of the pig.