The endemic Mauritian flying fox Pteropus niger is perceived to be a major fruit pest. Lobbying of the Government of Mauritius by fruit growers to control the flying fox population resulted in national culls in 2015 and 2016, with a further cull scheduled for 2018. A loss of c. 38,318 individuals has been reported and the species is now categorized as Endangered on the IUCN Red List. However, until now there were no robust data available on damage to orchards caused by bats. During October 2015–February 2016 we monitored four major lychee Litchi chinensis and one mango ( Mangifera spp.) orchard, and also assessed 10 individual longan Dimocarpus longan trees. Bats and introduced birds caused major damage to fruit, with 7–76% fruit loss (including natural fall and losses from fungal damage) per tree. Bats caused more damage to taller lychee trees (> 6 m high) than to smaller ones, whereas bird damage was independent of tree height. Bats damaged more fruit than birds in tall lychee trees, although this trend was reversed in small trees. Use of nets on fruiting trees can result in as much as a 23-fold reduction in the damage caused by bats if nets are applied correctly. There is still a need to monitor orchards over several seasons and to test non-lethal bat deterrence methods more widely.