We aimed to investigate the effect of CR with probiotic supplementation on weight loss and parameters related to the homeostatic and hedonic systems. It is a randomized, double-blind, parallel, placebo-controlled clinical trial (UTN: U1111-1247-9906). We include obese adult males, aged 25 to 44 years. The established CR was 30% of the daily energy expenditure. Probiotic supplementation was: two sachets of 1 g each of 1×10⁹ CFU of Lactobacillus acidophilus NCFM, Lactobacillus rhamnosus HN001, Lactobacillus paracasei Lpc-37, and Bifidobacterium lactis HN019. The primary outcomes: body composition. Secondary outcomes: leptin, ghrelin, GLP-1, glucose-dependent insulinotropic polypeptide (GIP), insulin, peptide YY (PYY), and adiponectin. Additionally, binge eating, emotional eating, and cognitive restraint were assessed by the Three-Factor Eating Questionnaire. The study includes per protocol analyses (CR + placebo [CRPLA] n = 12 vs. CR + probiotic [CRPRO] n = 13). Body mass (F = 65.9; p < 0.001) decreased after 4 and 12 weeks (p < 0.001). A similar result was found for absolute fat mass (F = 71.0; p < 0.001) after 4 and 12 weeks (p < 0.001). Leptin levels decreased (F = 13.2; p < 0.001) after 4 (p = 0.002) and 12 weeks (p < 0.001), without group or interaction effect. Moreover, GLP-1 levels did not change after intervention (F = 2.29; p = 0.114). Likewise, GIP (F = 2.0; p = 0.148) and adiponectin (F = 3.14; p = 0.053) levels did not change. Binge eating reduced (F = 16.5; p < 0.001) only in the CRPRO group (p = 0.018). Emotional eating decreased (F = 9.44; p = 0.005), but only in the CRPRO group (p = 0.047). Finally, cognitive restraint increased (F = 43.2; p < 0.001) in the CRPLA (p = 0.003) and CRPRO (p < 0.001) groups. In summary, CR reduced body mass and body fat, as well as decreased leptin levels and increased cognitive restraint. Additionally, reductions in binge eating and emotional eating scores were seen only in the CRPRO group.