Chemical permeabilization has been widely studied for the release useful metabolites from many types of plant cells and tissues. In this study, the effect of 0−30% (v/v) of aqueous methanol solutions were used to permeabilize soybeans for the release of two isoflavonoids: daidzein and genistein. The release of these metabolites increases with increasing methanol concentrations. The amounts of daidzein and genistein released can increase up to 40- and 86-fold, respectively, when incubated in a 30% (v/v) methanol solution for 24 h compared with those incubated with water only. The effect of methanol on the release rates is primarily due to an increase in solubility of the stored daidzein and genistein (14- to 18-fold) inside the seeds, thus maximizing the concentration gradients for metabolite release. However, the viability of the seeds dropped with increase in methanol concentrations and the incubation time. The viability of soybeans (indicated by their ability to germinate) after permeabilization treatment with 0−20% (v/v) methanol solutions was maintained above 80% throughout the 24 h, whereas no seeds were found to be viable when 30% (v/v) methanol solution was used. The permeability coefficients (P) of daidzein and genistein were found to increase as the methanol concentration used was increased. These P values were estimated to range from 1.1 × 10−9 to 1.9 × 10−8 m/s and 1.0 × 10−9 to 1.7 × 10−8 m/s, respectively. The increase in Pcan be attributed primarily to an increase in the partition coefficient of the metabolites in the soybean seedcoats. An empirical correlation is proposed in which the log Pvalues are described as a function of the metabolite molecular weights and the partition coefficients of the metabolites between octanol and water, Koct/water, which was modified to include the effect of methanol present. Knowledge obtained from this study will help provide useful selection criteria for chemical permeabilization of plant tissues, such as seeds, with minimal loss in their viability.