Self-directed behavior, such as self-scratching (hereafter, scratching), occurs in several taxa across the animal kingdom, including nonhuman primates. There is substantial evidence that scratching is an indicator of anxiety-like emotions in a variety of nonhuman primate species. Despite its importance as a window into emotional states, few studies have investigated scratching in Platyrrhines. We investigated scratching patterns of 24 Geoffroy's spider monkeys (Ateles geoffroyi) belonging to a group living in the Otoch Ma'ax Yetel Kooh protected area in the Yucatàn peninsula (Mexico). We assessed whether scratching could be used as an indicator of anxiety levels in this species by testing predictions based on contexts and behaviors associated with risk and uncertainty. We found no effect of the subject's sex and age, subgroup size, male presence, and the occurrence of fusions between subgroups on scratching rates. Similarly, we found no effect of infant proximity on their mother's scratching rates. Supporting our prediction, we found evidence that isolation from conspecifics affected scratching rates as individuals scratched more frequently the more time they spent isolated. Being in proximity with a partner with a relationship characterized by uncertainty affected scratching rates as individuals scratched more frequently when in proximity with a partner with whom they engaged in embraces (an indicator of uncertainty) than when in proximity with a partner with whom they did not exchange embraces. Our study provides insight into the factors affecting scratching in Geoffroy's spider monkeys, suggesting that scratching may indicate anxiety in this species at least in some contexts and thus opening a window into the emotional experience of another Platyrrhine monkey species.