Consumers differentiate milk-quality characteristics in relation to the production system, but data on retail milk composition are limited. This study investigated how farming methods and seasons affect proximate composition, fatty acid profile, antioxidant activity, and physicochemical characteristics of commercial cow’s milk. Milk samples, both conventional (n = 84, 7 manufacturers) and organic (n = 24, 2 manufacturers), were collected monthly over a year. Farming system did not significantly affect milk composition other than fat content, whereas seasonal effects were notable, impacting the contents of ash, protein, and added water. Fatty acid composition exhibited variations influenced by both production system and season. Compared to conventionally produced milk, organically produced milk exhibited higher levels of polyunsaturated fatty acids (4.54 vs. 3.88, p < 0.01) and a lower atherogenicity index (2.23 vs. 2.50, p < 0.05). The antioxidant activity showed that conventionally produced milk exhibited better radical-scavenging activity (DPPH) (14.54 vs. 12.30 μM TE/mL, p < 0.01). Seasonal variations were evident in both free radical-scavenging activity (DPPH), with values of 12.29 μM TE/mL in winter and 15.58 μM TE/mL in spring (p < 0.05), and ferric reducing-antioxidant power (FRAP), with levels of 21.81 μM TE/mL in autumn and 27.94 μM TE/mL in spring (p < 0.05). Season significantly affected (p < 0.001) milk pH, electrical conductivity, refractive index, and freezing-point depression. In conclusion, this study showed that the farming system has a limited impact on retail milk quality compared to the significant influence of season.