Obesity is becoming a pandemic and percutaneous electrical stimulation (PENS) of dermatome T6 has been demonstrated to reduce stomach motility and appetite, allowing greater weight loss than isolated hypocaloric diets. However, modulation of intestinal microbiota could improve this effect and control cardiovascular risk factors. Our objective was to test whether addition of probiotics could improve weight loss and cardiovascular risk factors in obese subjects after PENS and a hypocaloric diet. A pilot prospective study was performed in patients (n = 20) with a body mass index (BMI) > 30 kg/m2. Half of them underwent ten weeks of PENS in conjunction with a hypocaloric diet (PENS-Diet), and the other half was treated with a PENS-Diet plus multistrain probiotics (L. plantarum LP115, B. brevis B3, and L. acidophilus LA14) administration. Fecal samples were obtained before and after interventions. The weight loss and changes in blood pressure, glycemic and lipid profile, and in gut microbiota were investigated. Weight loss was significantly higher (16.2 vs. 11.1 kg, p = 0.022), whereas glycated hemoglobin and triglycerides were lower (−0.46 vs. −0.05%, p = 0.032, and −47.0 vs. −8.5 mg/dL, p = 0.002, respectively) in patients receiving PENS-Diet + probiotics compared with those with a PENS-Diet. Moreover, an enrichment of anti-obesogenic bacteria, including Bifidobacterium spp, Akkermansia spp, Prevotella spp, and the attenuation of the Firmicutes/Bacteroidetes ratio were noted in fecal samples after probiotics administration. In obese patients, the addition of probiotics to a PENS intervention under a hypocaloric diet could further improve weight loss and glycemic and lipid profile in parallel to the amelioration of gut dysbiosis.