This study aimed to produce fermented soy-powder milk (FSPM) with Lactobacillus plantarum P1201 and to evaluate its anti-obesity activity. Isoflavone and conjugated linoleic acid (CLA) of unfermented soy-powder milk (UFSPM) and FSPM and were analyzed via high-pressure liquid chromatography (HPLC) and gas chromatography (GC). Their inhibitory activities against α-glucosidase, α-amylase, and pancreatic lipase were assayed. Their anti-obesity activities were evaluated on the basis of their inhibitory effects on adipocyte differentiation in 3T3-L1 cells, and the expression of mRNAs associated with adipogenesis and lipid metabolism were analyzed via real time-polymerase chain reaction (RT-PCR) and quantitative PCR (qPCR). FSPM with L. plantarum P1201 increased the isoflavone aglycones (daidzein, glycitein, and genistein) content and produced CLA in soy-powder milk (SPM), both of which possessed bio-activity. Both UFSPM and FSPM showed dose-dependent inhibitory activity for α-glucosidase, α-amylase, and pancreatic lipase. FSPM, but not UFSPM, suppressed adipogenesis in 3T3-L1 cells and reduced their triglyceride content by 23.1% after treatment with 1,000 μg/mL of FSPM, compared with the control group. The anti-obesity effect of FSPM can be attributed to CLA and isoflavone aglycones, which targeted CCAAT/enhancer binding protein α (C/EBP-α) and down-regulated lipoprotein lipase (LPL), adiponectin, adipocyte fatty acid-binding protein (aP2), fatty acid synthase (FAS), and acetyl CoA carboxylase (ACC) mRNA. Furthermore, FSPM enhanced the inhibitory activity of glucosidase and pancreatic enzymes and anti-obesity activity. Further studies are required to investigate whether the anti-obesity effect of FSPM persists in an in vivo mouse model of diet-induced obesity.