Abstract Egyptian fruit bats are experimental animals of increasing interest because they have been identified as a natural reservoir for several emerging zoonotic viruses. For this reason, bats could undergo different experimental procedures that require sedation or anaesthesia. Our aim was to compare the effects of two balanced anaesthetic protocols on sedation, cardiopulmonary variables and recovery in bats undergoing gonadectomy. Twenty bats were randomized into two groups; patients in group DK received intramuscular injection of dexmedetomidine (40 μg kg -1 ) and ketamine (7 mg kg -1 ), whereas those in group DBM were anaesthetized with intramuscular dexmedetomidine (40 μg kg -1 ), butorphanol (0.3 mg kg -1 ) and midazolam (0.3 mg kg -1 ). Time of induction, cardiopulmonary parameters and anaesthetic depth were measured. If anaesthesia plan was considered inadequate, fraction of inspired isoflurane was titrate-to-effect to achieve immobility. At the end of the surgery venous blood gas analysis was performed and intramuscular atipamezole (200 μg kg -1 ) or atipamezole (200 μg kg -1 ) and flumazenil (0.03 mg kg -1 ) was administered for timed and scored recovery phase. A significantly higher heart rate and peripheral oxygen saturation were recorded in DBM group ( p = 0.001; p = 0.003 respectively), while respiratory rate was significantly lower than DK group ( p = 0.001). All bats required isoflurane supplementation during surgery with no significant difference. No differences were observed in rectal temperature, induction and recovery times. Sodium and chlorine where significantly higher in DBM group ( p = 0.001; p = 0.002 respectively). Recovery scores in group DK were significantly better than in group DBM ( p = 0.034). Both protocols induced anaesthesia in Egyptian fruit bats with comparable sedative and cardiorespiratory effect. These drug combinations may be useful for minor procedures in bats, and they could be associated with inhalation anaesthesia in determining and maintaining a surgical anaesthetic plan.