Increased consumption of dietary supplements brings about important requirements of analytical methods to allow accurate and precise measurements of the chemical composition of these botanical materials. Presented here is the isoflavone content in proposed National Institute of Standards and Technology standard reference materials (SRMs) determined by LC-particle beam/electron ionization MS. Botanical materials (soy, red clover, and kudzu) are characterized for the content of a suite of five isoflavones (puerarin, daidzein, genistein, formononetin, and biochanin A). These compounds are of interest due to correlations with certain health benefits. An RP chromatographic separation was first optimized using UV-Vis spectrophotometric detection. The LC output was then introduced to an electron ionization source using a particle beam interface on an Extrel Benchmark MS system. The separation was carried out using a commercial C18 column and a linear gradient using water and methanol (both containing 0.1% trifluoroacetic acid as mobile phases A and B, at a flow rate of 1.0 mL/min over 40 min. LOD values for the isoflavones were determined to be at the ng level. Quantitation was performed using an internal standard (IS) approach with 7-hydroxy-4-chromone as the IS compound. The levels of isoflavones in the botanical products were determined for the proposed SRMs.