Background: Disruptive behavior and emotional problems – especially anxiety – are common in children and frequently co-occur. However, the role of co-occurring emotional problems in disruptive behavior intervention response is unclear. This study aimed to compare the effectiveness of an indicated prevention program in children with disruptive behavior problems with vs. without co-occurring emotional problems. Methods: Children were screened for disruptive behavior and emotional problems during routine health check-ups and – if indicated – were offered a child-centered group prevention program. For children with disruptive behavior the “Baghira training” was administered. Training effectiveness was compared between participating children with vs. without emotional problems regarding disruptive behavior and emotional problems and anxiety in particular. Outcomes were measured before and after the training, and at six months follow-up using linear mixed effect model regression analyses. Results: Overall, regarding disruptive behavior, children with and without co-occurring emotional problems profited equally from the Baghira training and training effectiveness was independent of the pre-training level of anxiety. However, there were few indications for greater disruptive behavior symptom reduction in children with co-occurring emotional problems. Overall, the Baghira training had little to no effect on the examined emotional problems/anxiety measures, except the Strengths and Difficulties Questionnaire emotional problems score strongly decreased in children with co-occurring emotional problems. Conclusions: The effectiveness of the Baghira training is not negatively affected by co-occurring emotional problems/anxiety. However, as emotional problems/anxiety do not simultaneously improve, an additional training targeting these problems for respective children seems necessary.