Witch's broom, caused by the phytopathogen Moniliophthora perniciosa, is one of the most destructive fungal diseases affecting copoazú (Theobroma grandiflorum) cultivation in the Colombian Amazon region. This study aimed to evaluate rehabilitation pruning as a method for managing witch's broom in an agroforestry system with copoazú. The incidence, severity, and the relationship between environmental variables and disease progression were assessed using two different rehabilitation pruning methods and a control (crop without intervention). Evaluations were conducted during two different periods of the year: the dry season and the rainy season. Highly significant statistical differences (P < 0.0001) were found for all evaluated factors in both incidence and severity (treatments, season, and their interaction). Treatment 2, which involved rehabilitation pruning with four branches retained, showed the lowest mean values with an average incidence of 4.4% and severity of 0.08. During the dry season, the lowest values for both variables were observed. Regarding the relationship between the progression of witch's broom disease and environmental variables, a high correlation was found between disease incidence and severity with relative humidity and precipitation. This indicates favorable conditions for the advancement of witch's broom in copoazú plantations in the Colombian Amazon region. In conclusion, rehabilitation pruning in copoazú cultivation appears to be an effective method for controlling witch's broom in the Colombian Amazon region.