Background Hendra virus (HeV) infection is endemic in Australian flying-fox populations. Habitat loss has increased the peri-urban presence of flying-foxes, increasing the risk of contact and therefore viral ‘spillovers’ into horse and human populations. An equine vaccine is available and horse-husbandry practices that minimize HeV exposure are encouraged, but their adoption is suboptimal. Ecological approaches–such as habitat creation and conservation–could complement vaccination and behavioural strategies by reducing spillover risks, but these are controversial. Methods We convened three community juries (two regional; one metropolitan) to elicit the views of well-informed citizens on the acceptability of adding ecological approaches to current interventions for HeV risk. Thirty-one participants of diverse backgrounds, mixed genders and ages were recruited using random-digit-dialling. Each jury was presented with balanced factual evidence, given time to ask questions of expert presenters and, after deliberation, come to well-reasoned conclusions. Results All juries voted unanimously that ecological strategies should be included in HeV risk management strategies but concluded that current interventions–including vaccination and changing horse-husbandry practices–must remain the priority. The key reasons given for adopting ecological approaches were: (i) they address underlying drivers of disease emergence, (ii) the potential to prevent spillover of other bat-borne pathogens, and (iii) there would be broader community benefits. Juries differed regarding the best mechanism to create/conserve flying-fox habitat: participants in regional centres favoured direct government action, whereas the metropolitan jury preferred to place the burden on landholders. Conclusions Informed citizens acknowledge the value of addressing the drivers of bat-borne infectious risks but differ substantially as to the best implementation strategies. Ecological approaches to securing bat habitat could find broad social support in Australia, but disagreement about how best to achieve them indicates the need for negotiation with affected communities to co-develop fair, effective and locally appropriate policies.