Biotransformation, the structural modification of chemical compounds, has proved to be an indispensable tool in providing beneficial health effects. Although the health benefits of biotransformation using plant sources has been widely studied, the anti-adipogenic effect of biotransformed dairy products, such as whey, have not yet been demonstrated. Here, we investigated the anti-adipogenic effect of whey biotransformed by Weissella cibaria in 3T3-L1 adipocytes. Weissella cibaria-biotransformed whey considerably reduced the accumulation of lipid droplets and intracellular triglycerides in 3T3-L1 cells. In the presence of W. cibaria-biotransformed whey, the mRNA and protein expression of a key transcription factor, peroxisome proliferator-activated receptor γ (PPARγ), for adipogenesis was markedly suppressed in 3T3-L1 cells. Additionally, W. cibaria-biotransformed whey also decreased the mRNA and protein expressions of lipoprotein lipase and adipocyte fatty acid-binding protein, which are regulated by PPARγ. Moreover, W. cibaria-biotransformed whey inhibited the expression of adipokines, resistin, and leptin. Collectively, these results suggest that whey biotransformed by W. cibaria has the potential to exert anti-adipogenic effects by inhibiting intracellular signaling events of adipogenic-related transcription factors and target genes.