Gut dysbiosis poses a significant public health concern, and malnutrition plays a central role in its development. In our recent clinical trial, we explored the effects of regulated walnut intake on the levels of 11 fecal metabolites to determine whether (I) walnut consumption promotes changes in metabolite profiles consistent with reduced gut dysbiosis, and (II) whether these changes are associated with the levels of urolithin A, a bioactive metabolite produced by colonic microbes following walnut consumption. DNA was extracted from fecal samples using a DNeasy 96 PowerSoil Pro QIAcube HT for 16S rRNA sequencing, and fecal short-chain fatty acids (SCFAs) and p-cresol were extracted fecal specimens by liquid chromatography/mass spectrometry (LC/MS-MS). At baseline, obese individuals (BMI > 30) had lower alpha diversity, higher p-cresol and valeric acid levels, and a higher trending Firmicutes to Bacteroidetes (F/B) ratio compared to non-obese (BMI < 30) participants, indicating a level of inherent gut dysbiosis. Walnut intake was associated with an overall 2.8% increase in alpha diversity, a 17.6% reduction in estimated marginal mean F/B ratio, and an overall reduction in three luminal proteolytic metabolites associated with gut dysbiosis: isobutyric acid, valeric acid, and isovaleric acid. Interestingly, the effects on the gut metabolome were more pronounced in obese individuals, with significant decreases observed in the same three SCFAs, as well as p-cresol. Given the known associations between these luminal proteolytic metabolites and gut dysbiosis, these results suggest that walnut intake may help to attenuate overall gut dysbiosis, particularly in obese populations.