Geoffroy’s spider monkeys, an endangered, fast-moving arboreal primate species with a large home range and a high degree of fission–fusion dynamics, are challenging to survey in their natural habitats. Our objective was to evaluate how different flight parameters affect the detectability of spider monkeys in videos recorded by a drone equipped with a thermal infrared camera and examine the level of agreement between coders. We used generalized linear mixed models to evaluate the impact of flight speed (2, 4, 6 m/s), flight height (40, 50 m above ground level), and camera angle (−45°, −90°) on spider monkey counts in a closed-canopy forest in the Yucatan Peninsula, Mexico. Our results indicate that none of the three flight parameters affected the number of detected spider monkeys. Agreement between coders was “substantial” (Fleiss’ kappa coefficient = 0.61–0.80) in most cases for high thermal-contrast zones. Our study contributes to the development of standardized flight protocols, which are essential to obtain accurate data on the presence and abundance of wild populations. Based on our results, we recommend performing drone surveys for spider monkeys and other medium-sized arboreal mammals with a small commercial drone at a 4 m/s speed, 15 m above canopy height, and with a −90° camera angle. However, these recommendations may vary depending on the size and noise level produced by the drone model.