Phytoestrogens are hormone-like substances in plants that can substantially influence human health (positively or negatively), and when fed to dairy cows are partly transferred to their milk. The aim of this study was to investigate the effects of varying the botanical composition and regrowth interval of legume-grass silage on phytoestrogen intake and milk phytoestrogen concentrations. In one experiment, 15 Swedish Red dairy cows were fed 2- or 3-cut red clover-grass silage, or 2-cut birdsfoot trefoil-grass silage. In a second experiment, 16 Norwegian Red dairy cows were fed short-term ley silage with red clover or long-term ley silage with white clover, and the effects of supplementation with α-tocopherol were also tested. High concentrations of formononetin and biochanin A were found in all silage mixtures with red clover. The milk concentration of equol was highest for cows on the 2-cut red clover-grass silage diet (1,494 μg/kg of milk). Because of the metabolism of biochanin A, genistein, and prunetin, their concentrations in milk and the apparent recovery were low. Coumestrol was detected in only short-term and long-term ley silage mixtures, and its milk concentration was low. Concentrations of secoisolariciresinol and matairesinol were higher in 2-cut birdsfoot trefoil-grass and long-term ley silage mixtures, those with legume species other than red clover, and the highest grass proportions. The 2-cut birdsfoot trefoil-grass silage diet also resulted in higher enterolactone concentration than the other diets (226 μg/kg of milk). Lengthening the regrowth interval increased the intake of secoisolariciresinol and decreased the recovery of lignans. Feeding long-term ley silage resulted in higher milk lignan concentrations but lower milk isoflavone concentrations than feeding short-term ley silage. The apparent recovery of all phytoestrogens except prunetin was highest on the 2-cut birdsfoot trefoil-grass silage diet. No effect of α-tocopherol supplementation was observed on milk concentrations of any of the measured phytoestrogens. Variations were observed in milk concentrations of phytoestrogens, especially of equol, among cows, which could not be explained by variations in diet composition or phytoestrogen intake. The results show that milk phytoestrogen concentration is strongly influenced by silage botanical composition, but questions regarding phytoestrogen metabolism remain to be answered.