The objective of this work was to study the effect of dairy system, herd within dairy system, and characteristics of individual cows (parity, days in milk, and daily milk yield) on the volatile organic compound profile of model cheeses produced under controlled conditions from the milk of individual cows of the Brown Swiss breed. One hundred fifty model cheeses were selected from 1,272 produced for a wider study of the phenotypic and genetic variability of Brown Swiss cows. In our study, we selected 30 herds representing 5 different dairy systems. The cows sampled presented different milk yields (12.3–43.2 kg/d), stages of lactation (10–412 d in milk), and parity (1–7). In total, 55 volatile compounds were detected by solid-phase microextraction and gas chromatography-mass spectrometry, including 14 alcohols, 13 esters, 11 free fatty acids, 8 ketones, 4 aldehydes, 3 lactones, 1 terpene, and 1 pyrazine. The most important sources of variation in the volatile organic profiles of model cheeses were dairy system (18 compounds) and days in milk (10 compounds), followed by parity (3 compounds) and milk yield (5 compounds). The model cheeses produced from the milk of tied cows reared on traditional farms had lower quantities of 3-methyl-butan-1-ol, 6-pentyloxan-2-one, 2-phenylethanol, and dihydrofuran-2(3H)-one compared with those reared in freestalls on modern farms. Of these, milk from farms using total mixed rations had higher contents of alcohols (hexan-1-ol, octan-1-ol) and esters (ethyl butanoate, ethyl pentanoate, ethyl hexanoate, and ethyl octanoate) and lower contents of acetic acid compared with those using separate feeds. Moreover, dairy systems that added silage to the total mixed ration produced cheeses with lower levels of volatile organic compounds, in particular alcohols (butan-1-ol, pentan-1-ol, heptan-1-ol), compared with those that did not. The amounts of butan-2-ol, butanoic acid, ethyl-2-methylpropanoate, ethyl-3-methylbutanoate, and 6-propyloxan-2-one increased linearly during lactation, whereas octan-1-ol, 3-methyl-3-buten-1-ol, 2-butoxyethanol, 6-pentyloxan-2-one, and 2,6-dimethylpyrazine showed a more complex pattern during lactation. The effect of the number of lactations (parity) was significant for octan-1-ol, butanoic acid, and heptanoic acid. Finally, concentrations of octan-1-ol, 2-phenylethanol, pentanoic acid, and heptanoic acid increased with increasing daily milk yield, whereas dihydrofuran-2(3H)-one decreased. In conclusion, the volatile organic compound profile of model cheeses from the milk of individual cows was affected by dairy farming system and stage of lactation and, to lesser extent, by parity and daily milk yield.