This study aimed to evaluate the effect of production system and lactation stage (LS) on the yield, centesimal composition, and fatty acid profile of milk from Holstein–Friesian cows. A total of 539 milk samples were collected in winter from cows in six certified organic dairy herds (ODHs) and eight conventional dairy herds (CDHs). The samples were collected randomly from up to 30% of cows at a given stage of lactation (7–45, 46–90, 91–135, 136–180, 181–225, 226–270, 271–315, and 316–360 days after calving). Milk samples were analyzed for proximate composition and the concentrations of fatty acids. The average daily milk yield was 11.4 kg higher (p < 0.01) in CDHs than in ODHs (28.1 kg vs. 16.7 kg). The concentrations of milk fat, protein, and lactose were also higher in CDHs than in ODHs. The fatty acid profile of milk fat was more desirable in ODHs than in CDHs (higher concentrations of polyunsaturated fatty acids (PUFAs), including n-3 PUFAs, trans-vaccenic acid, linolenic acid, and conjugated linoleic acid, and a higher desaturase index). Milk yield decreased (the decrease was more pronounced in ODHs), the concentrations of milk constituents increased, and the proportion of short-chain fatty acids in milk fat decreased (p < 0.05) with advancing lactation.
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