Soy products contain abundant genistein and daidzein isoflavones. Orally ingested soy isoflavones are partially metabolized to isoflavan by enteric bacteria. Their levels in the blood increase after soy products are eaten. In this study, we investigated the influence of genistein, daidzein, and equol by intraperitoneal administration in lactating mice. Genistein decreased the secretion of α- and β-casein and downregulated the gene expression of Csn1, Csn2, Csn3, and Wap while inactivating the signal transducer and activator of transcription 5 (STAT5) and ERK1/2. In contrast, equol increased Csn1-3 expression while inactivating STAT3. Daidzein did not show inhibitory effects on milk production. The effects of genistein and equol were also confirmed in lactating mammary epithelial cells (MECs), which were cultured in the presence of soy isoflavones and equol at physiological concentrations for 7 days. These findings indicate that genistein, daidzein, and equol influence milk production in MECs in vivo and in vitro in distinctly different ways.