Dietary soy isoflavones have been shown to ameliorate insulin resistance and Type 2 diabetes. However, many in vitro studies used supra-physiological concentrations of individual isoflavones that make it difficult to interpret the results as potential mechanisms in vivo. Since the insulin-sensitizing effects of thiazolidinediones, anti-diabetic drugs, have been shown to be mediated through activation of peroxisome proliferators-activated receptor gamma (PPARγ), the key transcription factor for adipocyte differentiation, we examined the effects of the two main soy isoflavones genistein and daidzein either as individual compound or combined on adipocyte differentiation and PPARγ expression, as well as whether the Wnt/β-catenin signaling pathway is the underlying molecular mechanism. In 3T3-L1 cells, genistein and daidzein significantly enhanced adipocyte differentiation. Similarly the expression of PPARγ increased particularly at 20 µmol/L. The stimulatory effect is greater when the two isoflavones are combined, indicating a synergistic effect. Genistein and daidzein also increased the relative abundance of insulin-responsive glucose transporter 4 (GLUT4) mRNA with a greater effect when combined. Wnt10b expression was not affected by soy isoflavones treatments, while Wnt5b expression was only increased by the combination of genistein and daidzein. Our results suggest, that the combination of soy isoflavones has a greater effect in increasing the newly formation of adipocytes that are highly insulin-sensitive via an increase in PPARγ expression as well as increasing the expression of GLUT4. However, genistein and daidzein actions on Wnt signaling remain unclear. These data further support the epidemiological findings for the beneficial effect of soy consumption on insulin sensitivity.