The presence of plant lignans in 14 different soy-based health supplements is reported here for the first time together with the analysis of the isoflavone content, for which these products are commercialized. Six plant lignans, i.e., secoisolariciresinol, matairesinol, syringaresinol, lariciresinol, isolariciresinol, and pinoresinol, have been identified and quantified by gas chromatography-mass spectrometry, and a positive correlation has been found between the levels of plant lignans and the levels of isoflavones in the different products. Additional quantification of plant lignans and isoflavones in soybeans has been carried out, and results are provided to allow the comparison of the average levels in soybeans and soy-based supplements.