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Recently, patients with glycogen storage disease (GSD) have been described as having gut dysbiosis, lower fecal pH, and an imbalance in SCFAs due to an increase in acetate and propionate levels. Here, we report the fecal measurement of bacterial-related metabolites formic, acetic, lactic, propionic, and succinic acid, a key metabolite of both host and microbiota, on a previously described cohort of 24 patients (GSD Ia = 15, GSD Ib = 5, 1 GSD III = 1 and GSD IX = 3) and 16 healthy controls, with similar sex and age, using the high-performance liquid chromatography technique. The succinic acid levels were higher in the GSD patients than in the controls (patients = 38.02; controls = 27.53; p = 0.045), without differences between the groups for other metabolites. Fecal pH present inverse correlation with lactic acid (R = −0.54; p = 0.0085), while OTUs were inversely correlated with both lactic (R = −0.46; p = 0.026) and formic (R = −0.54; p = 0.026) acids. Using two distinct metrics of diversity, borderline significance was obtained for propionic acid, affecting the microbial structure on Euclidean basis in 8% (r2 = 0.081; p = 0.079), and for lactic acid, affecting 6% of microbial structure using Bray–Curtis distance (r2 = 0.065; p = 0.060). No correlation was found between SCFAs and total carbohydrate consumption among the participants or uncooked cornstarch consumption among the patients.