BackgroundTransition of dairy cows from a tied to a loose housing system may affect their behaviour, health and production. Such housing system changes have become more frequent in Estonia but knowledge is lacking on how cows adapt to a new system. The aim of this study was to evaluate how cows’ behaviour, milk production and composition, and different aspects of their health changed after transition from tied to loose housing.ResultsA herd of 400 dairy cows was moved to a new system on the same farm, so that effects of transport were not confounding factors. Behavioural observations were made for approximately 4 months following transition. Milk production data were recorded from 12 months before to 12 months after transition. Examination for skin alterations and cleanliness, as well as body condition scoring were carried out before transition, and thereafter monthly throughout the study. Significant effects on behaviour were observed just after the transition, with increases in the behaviour indicative of poor welfare, such as vocalisation and aggression, and decreases in those indicative of a good state of welfare, such as ruminating, resting and grooming. These effects were of short duration, with most returning to a steady state after the first week. Milk production declined already before the transition but fell significantly after transition, and this fall lasted longer in older cows. Likewise, somatic cell counts were higher in all cows following transition, but older cows were affected significantly more than cows in the first lactation. The frequency of lameness and skin alterations increased on average after transition. Body condition scores fell after transition but recovered by the second month. Therefore, there were adverse effects on the behaviour, health and production of the dairy cows transferred, although, apart from older cows, of short duration.ConclusionThe transition from tied to loose housing first had negative impacts on the welfare of the cows, although by the tenth day the behavioural indicators had returned to normal values. Impacts were more severe in higher parity cows, indicating that the change was more of a challenge for older cows.The findings of this study suggest that animals’ behaviour and health should be more carefully observed within about 2 weeks after transition. It is quite likely that more and more farmers in Estonia and elsewhere will recognize the benefits of keeping their dairy cattle in loose housing, aimed at improving animal welfare and the value of the production chain.Supplementary InformationThe online version contains supplementary material available at 10.1186/s13028-023-00690-1.