Unusual or extraordinary circumstances can cause change to normal husbandry regimes and daily care of managed animals. Increased biosecurity due to disease risk, for example, results in animals experiencing restrictions. Outbreaks of Highly Pathogenic Avian Influenza (HPAI) have caused zoos to remove birds from their regular exhibits and manage them indoors or in covered enclosures to reduce the likelihood of an HPAI outbreak on site. To date, there has been little research on the impacts of such husbandry change on bird behaviour and welfare. This paper examines the effect of an HPAI-induced enforced housing order (HO) on the behaviour and physical condition of a flock of Chilean flamingos in a UK zoo. Using ZooMonitor to record flock-wide behaviour patterns and scoring plumage condition, we collected data on flamingos during a housing order, immediately after lifting of the HO, and after a period of acclimation to their regular routine. Results showed that flamingos were very inactive under a HO and after release, that abnormal, redirected foraging actions occurred during the HO and after release, and that flamingos were more alert under the HO. An increase in records of good plumage condition correlated with social behaviour, inactivity, higher temperatures, and rain. This research highlights the multifactorial influences on zoo animal behaviour and shows why information on the animals, their inputs, the behavioural outputs they present, and their physical attributes should all be gathered and evaluated together to best understand the influences of husbandry and management changes on behaviour and welfare.