Abstract Obesity has become a concerning problem in cats. Increasing evidence demonstrates the utility of metabolomics in identifying disease biomarkers and assessing the effects of nutritional interventions, although limited information exists regarding alterations in fecal metabolites in lean and obese domestic cats in response to different macronutrient content. In the current study, three extruded diets were formulated based on adult maintenance using an isoenergentic approach. These diets were created by adjusting the levels of identical ingredients to achieve a low-protein [LP; protein 28% metabolizable energy (ME), fat 40%ME, NFE 32% ME), a low-fat (LF; protein 42% ME, fat 30% ME, NFE 30% ME), and a low-carbohydrate (LC; protein 36% ME, fat 41% ME, NFE 23% ME] diet. Healthy neutered male adult cats [n = 18; body condition scores (BCS) 4 or 5 (lean, n = 9) and 8 or 9 (obese, n = 9)] were fed each diet for a period of 4 wk in a 3 x 3 Latin square design. Fecal samples from each cat were collected between d 22 and 28 of each treatment period. A total of 67 fecal metabolites in six groups (35 amino acids, 11 fatty acids, 10 sugars and sugar metabolites, 5 alcohols, 3 nitrogenous bases, and 3 others) were analyzed using 1H NMR spectroscopy. To evaluate the impact of body condition, diet and their interaction on each metabolite, proc GLIMMIX covariance structure was selected by the smallest Akaike information criterion value in SAS. The Shapiro-Wilk test was used to check normality and lognormal or beta distribution were applied when appropriate. Bonferroni correction post-hoc test was followed to correct Type I error. Statistical significance was considered at P < 0.05. In lean cats, significantly greater concentrations of fecal proteinogenic and branched-chain amino acids, such as methionine, valine, and L-lysine, as well as pyruvic acid and sugars (P < 0.05) were observed. This suggests that these metabolites may either be more actively fermented by bacteria or not utilized as extensively as in obese cats, potentially contributing to a reduction in obesity status. Regardless of body condition, there is a possibility of an enhanced activity in the tryptophan degradation pathway, leading to the greatest concentrations of fecal tryptophan (P = 0.04) in the LF diet, while the greatest fecal D-galactose (P = 0.04) in the LP diet was likely due to the greater dietary carbohydrate content. These observed results suggested that fecal metabolites were influenced by both body condition and diet; however, body condition had a more substantial impact on metabolite changes in cats, whereas no body condition and diet interaction were noted. Overall, the study indicated distinct fecal metabolic signatures in lean and obese cats subjected to different macronutrient diets and further research is warranted to validate the observed findings. Funding was provided by Champion Petfoods, Natural Sciences and Engineering Council of Canada and Mitacs Accelerate.