Forage crop silage fed to feed-restricted pregnant sows can enhance their welfare. Red clover (Trifolium pratense) with phytoestrogens (PE) can potentially cause reproduction disorders. Little is known about the metabolism of PE in sows and their capacity to produce equol. This study examined faecal and urinary excretion of PE and equol in sows-fed red clover silage. During a four-week period, eight pregnant sows received red clover silage (RC) rich in PE (10.9 g/kg DM), and eight sows without red clover silage (C). Contents of PE were determined with microwave-assisted and solid-phase extraction and ultra-high-performance liquid chromatography. RC sows efficiently produced equol (on average 190.2 mg/kg DM in faeces and 171.5 µg/mg creatinine in urine). Excreted PE and equol conjugated and urinary equol reached a stable value over time (w1 = 119.1; w2 = 153.3; w3 = 208.8; w4 = 204.8 µg/mg creatinine), indicating an effective adaptation and elimination of equol and reduced risk for hormonal disturbances.