Drones are increasingly used for monitoring wildlife, and it is therefore necessary to evaluate their impact on animal behavior. According to the landscape of fear framework, animals assess and respond to perceived risks in their environment by adjusting their behavior and space use to avoid potential threats. Understanding how drones influence risk perception is thus crucial to avoid generating stress and altering the animal’s natural behavior. Geoffroy’s spider monkeys (Ateles geoffroyi) are endangered arboreal primates, but information on their distribution and abundance is scarce throughout their geographical distribution. Drones can aid to rapidly obtain such information, but data of their impact on the monkeys are needed to design surveys that minimize disturbance (i.e., any interference or modification of the natural behavior of the monkeys caused by the presence and operation of drones). Here, we evaluated whether drone flights influenced the following spider monkey behaviors: agonistic displays, self-scratching, whinny vocalizations, feeding, resting, social interactions, and moving. We also evaluated the effect of three flight parameters, flight height (35, 50 m above ground level), speed (2, 4 m/s), and distance to the drone (“close”, “medium”, and “far”) on spider monkey behavior and examined whether repeated exposure to drones resulted in tolerance (i.e., lack of a behavioral response). We found that drone flights influenced only agonistic displays and resting and that the only flight parameter affecting behaviors was the distance between the monkeys and the drone. We found that spider monkeys developed a tolerance to drone flights only for agonistic displays. Based on our results, we suggest that spider monkeys do not perceive drone flights as major sources of disturbance (such as predators) in the short term, and that drone monitoring can be a viable option to study this species if adequate flight protocols are implemented.