Peanuts have been reported to contain bioactive phytochemicals, particularly isoflavones (genistein, daidzein, and biochanin A) and trans-resveratrol. Currently, limited data are available regarding the levels of these bioactive compounds in peanuts with variations in reported levels. The purpose of this study was to compare four methods of extraction [stirring, sonication, Soxtec, and microwave-assisted sonication (MAS)] for runner peanuts. Quantification of the selected compounds was conducted by reverse-phase high-performance liquid chromatography (RP-HPLC). The results showed that the MAS and Soxtec methods extracted significantly higher amounts of the phytochemicals. Also, the defatted peanuts gave significantly higher amounts of the phytochemicals compared to the nondefatted peanuts. The high levels of the isoflavones may be attributed to heat-induced conversion of conjugate glycosides to aglycons. The MAS and Soxtec methods may be used for total isoflavone content quantitation, while sonication or stirring may be the method of choice for quantitation of isoflavone composition (aglycons and glycoside conjugates) in peanuts.