Pteropus lylei is known to form colonies up to 8,000 individuals (CITE) in trees that can become stripped of leaves by the bats' activity. The species has been documented to co-roost with Pteropus vampyrus in at least three of the four known roosts in Viet Nam where the largest mixed species colony (1,500 to 2,000 individuals) was historically found in the Doi pagoda, P. lylei was the more abundant species (Son et al. 2009). Most colonies for the species are located in close proximity to human populations where the roosts receive some degree of protection and foraging areas are available in the surrounding agricultural landscapes (Weber et al. 2015, Chaiyes et al. 2017, Choden et al. 2019, Duengkae et al. 2019). In Thailand, 53% of the roost sites were located within Buddhist temples (Chaiyes et al. 2017) where the bats receive some degree of protection during the day (Weber et al. 2015, Chaiyes et al. 2017, Duengkae et al. 2019). Similarly, many flying fox roosts in Cambodia are located in pagodas where monks provide protection from hunting (Choden et al. 2019). The roosting sites of P. lylei were at an average elevation of 23.73 m (0–81 m), and near rivers and water bodies (Chaiyes et al. 2017).
The species has been documented to travel from 2.2–23.6 km between day roosts and foraging areas (Weber et al. 2015) and in some landscapes, it may travel up to 105 km between colonies (Choden et al. 2019). In Kandal, Cambodia, radio tagged bats flew ca 20 km from the roost to the foraging area which were often in residential areas (53.7%) and plantations (26.6%), traveling an average of 28.3 km per night (range 6.9–105 km, Choden et al. 2019). In Cambodia, 6 of 14 tagged P. lylei used a second roost site for at least one night (Choden et al. 2019) and relatively frequent movements among colonies in Thailand have resulted in high levels of genetic connectedness of the broader species distribution in the region (Sukgosa et al. 2018).

Once individuals arrive at their foraging area, they make small-scale movements within their foraging area and appear to exhibit high foraging area fidelity within a season (Weber et al. 2015). Although most tracked bats foraged in farmland, plantations, and gardens, research indicates that small remnants of mangroves are important habitats of P. lylei (Weber et al. 2015). The species has a fairly diverse diet (34 food plant species) of exotic crops and native plants available in a landscape (Weber et al. 2015). As it feeds extensively in orchards, it is considered a pest in Thailand (S. Bumrungsri pers. comm.).

Pteropus lylei have been found to have unusually high antibody titers to the Nipah Virus, suggesting that it circulates in this species in Thailand and Cambodia (Wacharapluesadee et al., 2005).
Nothing is known of the species ecology in China (Smith et al. 2008), but it is logical to assume similar patterns are observed. Research is needed to fully understand the species distribution, ecology, habitat use, and population connectedness.

This species is known from Cambodia (Choden et al. 2019), central and eastern Thailand (Weber et al. 2015, Chaiyes et al. 2017, Sukgosa et al. 2018, Duengkae et al. 2019), and Viet Nam (Son et al. 2009). There is an unconfirmed record of the species in Yunnan in China (Smith et al. 2008).