This study analyzed gut microbiota and metabolite concentrations in fecal samples from dogs that underwent gastrointestinal resection to identify characteristic postoperative changes. Fecal samples were collected from four healthy dogs, four with lymphoplasmacytic enteritis (LPE), and sixteen that underwent resection. 16S rRNA gene sequencing and metabolomic analyses were performed. In the resection group, alpha diversity significantly decreased, and the relative abundances of Firmicutes, Fusobacteria, and Bacteroidetes declined. Among gastroduodenectomy cases, three dogs suspected of late complications showed lower levels of carbohydrates, amino acids, and vitamins, with a significant reduction in short-chain fatty acids (SCFAs), compared to those without complications. These three cases exhibited gut microbiota and metabolite profiles similar to the LPE group, suggesting a link to late complications. This study highlights distinctive changes in gut microbiota and metabolites after gastrointestinal resection, particularly SCFA reduction and shifts in SCFA-producing bacteria, which may contribute to late complications. This method may serve as a non-invasive approach for assessing risk factors and predicting late complications following gastrointestinal resection.