This article describes the development of topical hydrogels containing genistein-loaded nanoemulsions, obtained by means of spontaneous emulsification. This procedure yielded monodisperse nanoemulsions in a sub 250 nm range exhibiting negative zeta-potential and low viscosity. The formulations were incorporated into acrylic-acid hydrogels in order to have their viscosity adjusted for topical application. The semisolid formulations exhibit non-Newtonian pseudoplastic behavior. The skin permeation/retention of genistein from formulations was carried out using porcine ear skin mounted in Franz diffusion cells under sink conditions. The results showed a slow flow of genistein through the skin. Higher amount of genistein was detected into the skin from the formulation composed by medium chain triglycerides as oily core when compared to the octyldodecanol one. The overall results show that hydrogels containing genistein-loaded nanoemulsions could be considered as a promising formulation to delivery isoflavones into the skin.