To characterize the metabolic disorders of dairy cows treated with gossypol, 12 dairy cows were assigned to either a control group or a treatment group that was fed 1000 mg of gossypol per kilogram of dry matter feed for 28 days. Milk quality was adversely affected, as both milk protein and lactose levels were significantly decreased in the gossypol-treated group (3.40% vs 3.16%, P = 0.044; 5.15% vs 4.91%, P = 0.027; respectively). Plasma samples revealed increases in alanine aminotransferase (P = 0.092), choline esterase (P = 0.02), and glutathione transferase (P = 0.0005) and decreases in glucose (P = 0.076) in the gossypol-treated group. Mass spectrometry based comparative metabolomic analyses showed reduced concentrations of the gluconeogenesis precursor l-glutamine (P = 0.047), with significant decreases (P < 0.05) in plasma l-lysine, l-threonine, and homoserine levels after gossypol treatment. HDL-C and LDL-C levels in the gossypol-treated group were increased (P = 0.044) and decreased (P = 0.023), respectively. These results demonstrate that gossypol induced oxidative stress and hepatotoxicity; reduced peripheral lipid metabolism, and enhanced hepatic lipid accumulation; decreased amino acid bioavailability and milk protein synthesis; and decreased gluconeogenesis and milk lactose in dairy cows.