The Gomantong cave system, Kinabatangan, Sabah (Malaysia) hosts one of the largest bat colonies known from north Borneo. The nightly exodus of Chaerophon plicatus from this site is an economically valuable tourist attraction, and must impose significant controls on the regional ecology. Monitoring ecosystem health requires monitoring bat population size, but no quantitative assessments for the Gomantong colony are available in the literature. Traditional censusing techniques (based on packing density and roost area or on roost exodus counts) yield notoriously unreliable results. Here we have applied innovative image analysis and counting techniques to videographic, photographic and terrestrial laser scanning data obtained in July 2012. The colony exits in a consistent stream along a narrow exit trajectory. The laser scanning of the large cave entrance allowed precise measurement of bat position. Video data provided 0.02-second time resolution. Average flight speed was calculated (10.38 ± 0.85 m/sec), bat exit rate was estimated at three minute intervals (peaking at 14,000 bats/minute) and then summed over the 40 minutes of bat flight. The resultant colony size estimate of 275,625–276,939 (95% confidence interval) individuals of C. plicatus in Gomantong Caves in 2012 demonstrates that the technique is viable, provides a realistic basis for ecosystem management, and can be repeated to monitor ecosystem change. The estimated insect consumption by the colony of this size is 927 ± 191 metric tons of insects per year over an estimated 270 km² area, a very important component in maintaining ecosystem stability in the Gomantong Forest Reserve and the Kinabatangan Wildlife Sanctuary, as well as pest control over the large agricultural tracts of the region.