The murine 3T3-L1 pre-adipocyte cell line is widely used as an in vitro model for adipogenesis because of its similarities to primary fat cells. The aim of this study was to investigate the intracellular mechanisms by which skimmed milk fermented by two lactic acid bacteria (LAB), Enterococcus faecalis and Lactobacillus plantarum, inhibited the differentiation of 3T3-L1 pre-adipocytes. Skimmed milk fermented by both LAB, but not non-fermented skimmed milk, significantly reduced the accumulation of lipid droplets and cellular triglycerides in a concentration-dependent manner. The mRNA and protein levels of peroxisome proliferator-activated receptor γ (PPARγ) were markedly inhibited in the presence of skimmed milk fermented by both LAB. Furthermore, the skimmed milk fermented by both LAB decreased the mRNA and protein expressions of PPARγ-targeting genes, lipoprotein lipase and adipocyte fatty acid-binding protein. Under the same circumstances, resistin mRNA expression was downregulated, but not leptin mRNA expression. In contrast, skimmed milk fermented by both LAB significantly upregulated tumor necrosis factor-α (TNF-α). These results suggest that LAB-fermented skimmed milk inhibits adipogenesis by inhibiting a master transcription factor PPARγ via the upregulation of the proinflammatory cytokine TNF-α in 3T3-L1 cells.