Feeding extruded flaxseed (FLAX) and alfalfa protein concentrate (APC) to dairy cows increased milk omega-3 content but their effect on other milk components is not known yet. The objective of this study was to compare the effect of FLAX and APC in interaction with the level of concentrate on milk protein composition and Ca content. The corn silage based diets were composed with 30% (C0) or 65% concentrate (C+) and supplemented with FLAX (1 kg.d−1) or APC (2 kg.d−1). The diets supplied the same level of energy, protein and Ca. The trial was carried out according a nested reversed design using 24 dairy cows averaging 117 ± 14 DIM with 2 periods of 14 d. Data were analyzed according a split plot design using proc mixed procedure. The significance threshold was set at P ≤ 0.05. There was no significant interaction between the sources of omega 3 and the level of concentrate. C+ significantly increased milk yield (+ 3.7 kg), milk protein content (0.16%) and yield (141 g.d−1). C+ largely decreased casein/protein ratio (−2.6% units) and increased total and colloidal Ca (respectively +172 and +148 mg.kg−1). Increase in milk soluble protein might reflect a loss of integrity of mammary epithelium and/or a production of inflammatory proteins (such as haptoglobulin) associated with subacute ruminal acidosis. High level of concentrate could have induced bone mobilization to produce bicarbonate thus making more available Ca for mammary gland. Compared with FLAX, APC tended to decrease milk yield (0.9 kg.d−1, P = 0.061), despite no effect on DMI. APC increased both total protein and casein contents without impact on casein/protein ratio and protein yield. It decreased milk urea content. These results suggest that APC might have not changed the total supply of metabolic protein while reducing the supply of ruminal soluble nitrogen. APC decreased soluble Ca content. This result suggests that biodisponibility of Ca is lower for APC than for CaCO3 and minerals. This experiment shows that the source of omega-3 affects milk casein content whereas large increase of concentrate level does not increase milk casein content even though protein content increased.