The organism undergoes tremendous changes at the end of pregnancy and beginning of lactation. The aim of the study was to analyze the physiological changes in cows during the last month of a first pregnancy and the first 2 months of lactation, based on the protein expression in peripheral blood plasma. Changes were observed in the expression of proteins involved in lipid metabolism (apolipoprotein A-I, apolipoprotein E, apolipoprotein J, and apolipoprotein A-IV); immune defense (complement C4 protein and mannose-binding protein C); blood clotting (fibrinogen alpha chain, fibrinogen gamma B-chain, and fibrinogen-like protein 1); as well as reconstruction, regeneration, and defense of cells and tissues (fibrinogen-like protein 1, glutathione peroxidase 3, endopin-1, Kelch-like ECH-associated protein 1, 72 kDa type IV collagenase, and pigment epithelium-derived factor). Multidimensional changes in the cow organism observed on the protein level at the end of pregnancy and during the first months of lactation highlight the immense challenges the organism must overcome to maintain homeostasis.