Phytoestrogens, natural compounds with structural similarity to 17-β-estradiol, are known to have potential health benefits, including in hormone-dependent malignancies. The therapeutic interest and some safety concerns observed triggered the need to develop accurate methods to assess their level in different matrices. This narrative review examines the existing analytical methods used to isolate, quantify, and characterize phytoestrogens and their metabolites in plants, foods, and biological samples. Different conventional and modern extraction techniques, such as ultrasonication-assisted extraction, supercritical fluid extraction, or enzyme-assisted extraction, were presented and compared. The advantages and limitations of the existing analytical methods, such as high-performance liquid chromatography using different sensitive detectors, gas chromatography often coupled with mass spectrometry, and immunoassay methods, are highlighted, along with the need for ongoing research to improve the sensitivity and selectivity of the analysis.