Non-invasive behavioural indicators of welfare can be particularly useful for managing captive breeding populations of endangered species; these allow individual welfare to be monitored and reproductive success maximised without the need for capture and restraint methods. However, most studies focus on the behaviours whose presence or frequency can predict welfare issues; the absence of a behaviour is less frequently considered an indicator of welfare. Here, we investigate potential behavioural correlates with welfare-related health states in captive Livingstone’s fruit bats (Pteropus livingstonii), a critically endangered species that can become obese due to restricted space and reduced activity rates compared with wild populations. In this study, behavioural data were collected on males (which are particularly prone to obesity). Hurdle models were used to separately determine the factors predicting the presence or absence of behaviour and the frequency of observed behaviours. Whilst significantly lower levels of vigilance were observed in males with a larger body mass, those with diagnosed health issues were significantly more likely to show an absence of locomotion and foraging behaviour. Males with a lower body mass were also more likely to show an absence of foraging behaviour. Our study demonstrates how the absence of a behaviour can be informative as to an individual’s welfare state. This study has identified behavioural profiles that can be used to flag at-risk individuals, reducing the need for potentially stressful handling and improving our ability to safeguard the welfare of individuals within a large captive group.