Polyphenols are dietary bioactive compounds able to induce modifications in the gut microbiota profile, although more clinical studies are needed. With this aim, a randomized cross-over clinical trial was conducted, where 49 subjects at cardiometabolic risk (exhibiting at least two metabolic syndrome factors) were supplemented with a daily dose of 8 g of grape pomace (GP) for 6 weeks, with an equivalent control (CTL) period. The levels of total bacteria and Bacteroidetes, Firmicutes, Lactobacilliales, Bacteroides and Prevotella were estimated in fecal DNA by quantitative real-time PCR (qPCR), while fecal short-chain fatty acids (SCFAs) were assessed by gas chromatography. Several cardiometabolic markers were evaluated in blood samples. GP reduced insulin levels only in half of the participants (responders). GP supplementation did not cause significant modifications in the microbiota profile of the whole group, except for a tendency (p = 0.059) towards a decrease in the proportion of Lactobacilliales, while it increased the proportion of Bacteroides in non-responder subjects. The reduction of insulin levels in subjects at cardiometabolic risk upon GP supplementation appears not to be induced by changes in the major subgroups of gut microbiota. Further studies at the species level may help to elucidate the possible role of microbiota in GP-induced insulinemic status.