Green tea kombucha (GTK) has emerged as a promising probiotic fermented beverage. Few studies have investigated its effect on human health, mainly focusing on intestinal health, microbiota composition, and metabolomics. The present study is a pioneer in investigating the effect of GTK consumption in individuals with excess body weight. This is a randomized controlled trial, lasting ten weeks, with two groups placed under an energy-restricted diet: control (CG, n = 29), kombucha (KG, n = 30; 200 mL/d). Biological samples and questionnaires were collected before and after the intervention. Microbiota analysis used an amplification of the V4 region of 16S rRNA. Serum untargeted metabolomics used HPLC-TOF mass spectrometry. Intestinal permeability considered the urine excretion of lactulose and mannitol, plasma zonulin, and LPS-binding protein. After the intervention, no differences related to intestinal permeability and microbiota were found between groups, but only the CG had increased fecal pH, lactulose/mannitol ratio, and zonulin. In addition to this, the KG reported lower gastrointestinal symptoms related to motility compared to the CG, and discriminant metabolites (e.g., diethyl malonate) were found strictly in the KG. GTK did not significantly improve gut microbiota and intestinal permeability. However, GTK ameliorated gastrointestinal symptoms and positively influenced the serum metabolome, which may contribute to enhancing the metabolic health of individuals with excess body weight.