Estrogen is known to modulate certain cognitive functions, most notably improving working memory and verbal memory. Soy foods contain isoflavones, phytoestrogens structurally similar to estrogen that weakly bind to estrogen receptors. We investigated the effects of natural variations in estrogen levels and short-term dietary supplementation with soy isoflavones on cognitive function in 28 young women. Performance was examined across a range of cognitive tasks on three occasions during separate menstrual cycles: during a menses phase (low estrogen), during a luteal phase (highest estrogen), and once during a menses phase after a 3-day phytoestrogen-rich dietary intervention. Soy supplementation during menses led to an improvement in working memory and verbal memory. The menstrual cycle effects were mixed, with high estrogen improving performance on a verbal memory task but not on working memory. Our results suggest that soy phytoestrogens may improve working memory through estrogen-independent mechanisms.