The aim of the study was to evaluate selected indicators of protein metabolism in cows fed with fodder contaminated with mycotoxins after application of a mycotoxin deactivator product (MDP). Experimental group (Exp.)—10 cows, fed total mixed ration (TMR) containing: 0.769 mg/kg-deoxynivalenol and 0.032 mg/kg-zearalenone TMR DM. Control group (Con.)—10 cows fed TMR without mycotoxins. In the exp. cows, the mycotoxin deactivator product (MDP) Mycofix Plus was used in the form of an additive to TMR in the amount of 10 g/head/day for 90 days. Blood was taken in Exp. group three times, before MDP administration, and on days 30 and 90 of its use. In the con. group, blood was collected once. All cows were assessed for free amino acids, total protein, albumin, globulin, and urea. Cows with mycotoxicosis (before MDP administration) showed low total protein, albumin, total-essential (TEAA) and total-non-essential amino acids (TNEAA) compared to after MDP administration (p < 0.01). Compared to the control group, TNEAA values were lower and TEAA higher on all study dates (p < 0.001). The results of our research showed the negative impact of mycotoxins on the parameters of protein metabolism in cows, and the use of MDP improved the processes of protein metabolism and improved the overall health of cows.