Background: Disruptive behavior and emotional problems are common in children and often reduce quality of life. This study aimed to screen for these problems and to examine the effectiveness of child-based indicated prevention. Methods: N = 3231 children`s disruptive behavior and emotional problems were screened using the Strengths and Difficulties Questionnaire (SDQ) during routine pediatric health check-ups for usually 5- to 10-year old’s. We examined the prevalences of disruptive behavior and emotional problems (n = 2825) and its association with quality of life (KINDL; n = 1104). If indicated, children were recommended to participate in the prevention program “Baghira training” (nine 90 min group sessions and one parents’ evening) or “Tiger training” (two one-on-one and nine group sessions of 60 min each). To evaluate the training effectiveness of the two indicated prevention programs, SDQ and KINDL scores were followed-up for 6 and 12 months post screening and compared between the Training group (SDQ n = 337; KINDL n = 334; additionally divided into Baghira and Tiger), children not participating despite indication (NoTraining; SDQ n = 595; KINDL n = 146; additionally divided into NoBaghira and NoTiger), healthy children (SDQ n = 1928; KINDL n = 907), and children with clinical symptom levels (SDQ n = 85; KINDL n = 54) using mixed effect models. Results: 37.0% of the children exhibited disruptive behavior or emotional problems, which were associated with impaired quality of life. The Training group perceived greater symptom reduction in emotional problems than NoTraining, and quality of life increases compared to decreases in NoTraining. The Tiger group showed improvement in symptomatology and quality of life compared to deterioration in NoTiger. The Baghira group also improved, though improvement was similar to NoBaghira apart from symptom reduction in emotional problems in Baghira compared to a symptom increase in NoBaghira. Effects sizes were predominantly small to medium. Conclusions: Disruptive behavior and emotional problems in children are frequent and impair quality of life. Indicated prevention may improve symptomatology and quality of life. Specifically, the Tiger training is verifiably effective; for the Baghira training, effectiveness is implicated but needs further empirical evaluations.