Previous studies using probiotics have shown strain-dependent effects on body mass index (BMI), body mass, or fat mass (FM). The aim of this study was to evaluate how the addition of yogurt containing Lactobacillus acidophilus LA-5 and Bifidobacterium animalis subsp. lactis BB-12 strains to a diet plan affects selected anthropometric parameters in obese people on an energy-restricted diet. Fifty-four subjects aged 20–49 (34.52 ± 9.58) years were included in this study. The recruited subjects were assigned to two subgroups: consuming probiotic yogurt along with a hypocaloric diet (GP) (n–27) or the same diet but without an intentional introduction of yogurt (GRD) (n–27) for 12 weeks. Both GP and GRD decreased body weight, BMI, fat mass and visceral fat by 5.59 kg and 4.71 kg, 1.89 and 1.61 kg/m2, 4.80 kg and 4.07 kg, and 0.68 and 0.65 L, respectively, although the obtained differences were not significant. Analysis of GP and GRD results separately at the beginning and end of the intervention showed that fat loss was substantial in both groups (p < 0.05). Consumption of yogurt containing LA-5 and BB-12 does not significantly improve anthropometric parameters in obese patients.