Prepubertal gonadectomy (PPG) is promoted for population control in cats, but concerns related to health and behavior still exist. From a behavioral point of view, in order for PPG to be an acceptable alternative for traditional-age gonadectomy (TAG), the occurrence of undesirable behavior should be unaffected by age at gonadectomy. The aims of this study were to investigate (1) whether the average number of (potentially) undesirable behaviors in shelter kittens during 24 months after adoption was associated with the age at gonadectomy and (2) whether social or environmental factors were related to the occurrence of commonly reported undesirable behaviors (inappropriate elimination, fearfulness, aggression, and destruction). Eight hundred healthy kittens between the estimated age of 8 and 12 weeks (0.7 and 1.4 kg) were recruited from animal shelters in Flanders, Belgium. Before adoption, kittens were randomly assigned to a PPG group (gonadectomy on assignment) and a TAG group (gonadectomy between 6 and 8 months of age). Online short- and long-term follow-ups were conducted using a 30-day diary immediately after adoption and surveys at 2, 6, 12, 18, and 24 months after adoption. Mean number of potentially undesirable behaviors per day during the first month after adoption was not significantly different between PPG (1.48 ± 0.957) and TAG (1.39 ± 0.899) kittens (P = 0.32) and neither was the evolution of the mean number of potentially undesirable behaviors and undesirable behaviors during the long-term follow-up (P = 0.0946 and P = 0.10, respectively). The occurrence of inappropriate elimination, fearful behavior, non–play-related aggression, and destruction was associated with other social and environmental variables (e.g., the use of punishment by the owner and friendliness toward a stranger). In conclusion, this study in shelter cats did not demonstrate an effect of age at the time of gonadectomy on the mean number of (potentially) undesirable behaviors during 24 months after adoption. Other factors seem to play a more dominating role in the development of such behaviors.