Abstract BACKGROUND: The present study investigated tissue‐specific responses of muscle and mammary gland to a 10 week intervention of German Holstein cows ( n = 18) with three different dietary fat supplements (saturated fat; linseed oil or sunflower oil plus docosahexaenoic acid‐rich algae) by analysing fatty acid profiles and quality parameters of meat and milk. RESULTS: Plant oil/algae intervention affected neither fat content nor quality parameters of meat but decreased fat content and saturated fatty acid amounts of milk. Linseed oil/algae intervention caused significantly higher concentrations of C18:3 n ‐3 (meat, 1.0 g per 100 g; milk, 1.2 g per 100 g) and C22:6 n ‐3 (meat, 0.3 g per 100 g; milk, 0.14 g per 100 g). Sunflower oil/algae intervention increased n ‐6 fatty acid contents in milk (4.0 g per 100 g) but not in meat. Elevated amounts of C18:1 trans isomers and C18:1 trans ‐11 were found in meat and especially in milk of plant oil/algae‐fed cows. C18:1 cis ‐9 amounts were found to be increased in milk but decreased in meat after plant oil/algae intervention. CONCLUSION: The present study demonstrated that dietary fatty acid manipulation substantially shifted the fatty acid profiles of milk and to a lesser extent of meat, whereas meat quality traits were not affected. Indications of tissue‐specific responses of mammary gland and muscle were identified. Copyright © 2012 Society of Chemical Industry