Phytoestrogens are plant-produced secondary compounds that mimic the animal sex hormone estrogen. Several legumes, including red clover, produce phytoestrogens as stress defense molecules, and climate change-driven increases in atmospheric temperature and CO2 may intensify their production. We conducted a growth chamber study to determine the effects of short-term exposure to elevated temperature (eT) and CO2 (eCO2), both alone and in combination, on phytoestrogen concentrations in red clover and cowpea. Plants were grown in ambient conditions (24/18 °C, day/night, and ~ 400 ppm CO2) and then exposed to eT (35/26 °C, day/night), eCO2 (750 ± 50 ppm), or both factors for 10 days. Phytoestrogen concentrations in cowpea vegetative tissues were below the level of detection under all conditions. In red clover, exposure to eT reduced total phytoestrogen concentration by 50%, from 3.9 to 1.9 mg/g dry matter. Most of this decrease was driven by reduced concentrations of the isoflavones formononetin and biochanin A. Elevated CO2 did not influence total phytoestrogen levels in red clover but reduced daidzein concentration by 43%. Plant physiological variables measured concurrently with phytoestrogens were weakly correlated with concentrations of individual phytoestrogen compounds and total phytoestrogens in red clover.