ScopeTo examine whether a Mediterranean Diet (MedDiet) compared to the consumption of nuts in the context of a habitual non‐MedDiet exerts a greater beneficial effect on gut microbiota and fecal metabolites; thus, contributing to explain major benefits on cardiometabolic risk factors.Methods and ResultsFifty adults with Metabolic Syndrome are randomized to a controlled, crossover 2‐months dietary‐intervention trial with a 1‐month wash‐out period, following a MedDiet or consuming nuts (50 g day^‐1). Microbiota composition is assessed by 16S rRNA gene sequencing and metabolites are measured using Nuclear Magnetic Resonance (NMR) and liquid chromatography coupled to triple quadrupole mass spectrometry (LC‐qTOF) platforms in a targeted metabolomics approach.Decreased glucose, insulin and the homeostatic model assessment of insulin resistance (HOMA‐IR) is observed after the MedDiet compared to the nuts intervention. Relative abundances of Lachnospiraceae NK4A136 and an uncultured genera of Ruminococcaceae are significantly increased after the MedDiet compared to nuts supplementation. Changes in Lachnospiraceae NK4A136 are inversely associated with insulin levels and HOMA‐IR, while positively and negatively with changes in cholate and cadaverine, respectively.ConclusionsFollowing a MedDiet, rather than nuts, induces a significant increase in Lachnospiraceae NK4A136 and improves the metabolic risk. This genera seems to affect the bile acid metabolism and cadaverine which may account for the improvement in insulin levels.