The effect of milk production systems on the welfare of dairy cows has been studied worldwide, but studies that compare pasture-based, compost barn, and free stall systems, according to animal welfare, are more scarce. In this work, the welfare of 51 dairy herds, including 17 from each management system, was investigated through the application of the Welfare Quality^® protocol. Descriptive statistics and the Kruskal–Wallis non-parametric method were used to analyze variables. In the present work, the welfare of the evaluated herds was significantly better in the pasture-based system than in the confinement systems. However, the pasture-based system presented weaknesses in providing water resources. The compost barn had fewer animal welfare critical points than the free stall system, as well as it was better than the free stall in measures related to comfort and health. The free stall did not present better scores than the other systems. It is concluded that the welfare of dairy cows is affected by the rearing system, with better scores, in most measures, in the pasture-based system, followed by the compost barn and, finally, the free stall.