The aim of the study was to determine differences in the status of selected bioactive whey proteins and lipophilic vitamins in milk obtained from certified organic farms as compared to conventional farms (using traditional and intensive production systems). Significant relationships were noted with regard to production system and individual bioactive milk compounds, that is β‐lactoglobulin, lactoferrin, lysozyme, vitamins A, D3 and E, and β‐carotene (P = 0.001) and bovine serum albumin (BSA) (P = 0.016). Milk obtained from extensive farms, especially certified organic ones, was a valuable source of certain antioxidant compounds: β‐lactoglobulin (3.32 g/L), lactoferrin (123.8 mg/L), vitamin E (2.044 mg/L) and β‐carotene (0.257 mg/L) in the case of organic farms.