Background: Nipah virus (NiV) is an emerging pathogen that, unlike other priority pathogens identified by WHO, is endemic to Southeast Asia. It is transmitted through exposure to saliva, urine or excrement from Pteropus fruit bats or direct contact with intermediate animal hosts or human-to-human transmission. However, little is known about the circulation of NiV and its epidemiology in Cambodia. Methods and materials: An integrated approach was undertaken at two flying fox roosts in Kandal and Battambang provinces to study bat ecology, NiV circulation in bat and human population and human practices and perceptions from 2013 to 2016. Results: Our integrated study allowed us to generate extensive data on the different components of the complex socio-ecosystem of NiV. Flying fox population monitoring showed that mating, birthing and weaning periods occurred at the same periods each year: mating in November, birthing in April and weaning in June. A total of 20/3157 (0.63%) and 8/773 (1.03%) bat urine samples in Kandal and in Battambang were respectively confirmed positive for NiV by RT-PCR. Detection rate of NiV was higher during pregnancy and lactation phases between March and May. Pollen from flowers were identified in a majority of bat faecal samples from December to March while fruits were identified when NiV was detected in urine. GPS study showed that the maximum distance travelled per night ranged from 6.88–105 km. Most foraging locations were in residential areas and plantations. Sera collected from 164 people residing in Kandal and 254 people living in Battambang tested negative for NiV antibodies. Knowledge, attitude and practice survey reported some human practices could lead to exposure to NiV including eating partially eaten fruits, consumption of palm juice and hunting and consuming bats. Conclusion: Our findings help provide recommendations to interrupt potential transmission routes and limit the risk of emergence through environmental and behaviour chan