This research paper investigated the effects of specific educational treatment on the prevention of offending risk in students with severe cognitive impairments. It also examined the hypothesis of whether behavioral risk indicators were reduced by means of mediators like executive functioning, emotional regulation, social competence, and academic engagement. A quasi-experimental longitudinal design using the pretest-posttest control group was used. 120 students aged between 10 and 16 years were dispersed in either an intervention group (n = 60) or a comparison group (n = 60). The intervention involved the use of individualized education planning, training in cognitive-behavioral skill development, and executive functioning, as well as social-emotional learning, for 12 months. The behavioral, academic, and socio-emotional outcomes were measured both at the baseline and post-intervention. Mediation and repeated measures ANOVA were done. The incidence of disciplinary incidents was reduced in the intervention group by 42% as compared to 10 percent in the comparison group (p < 0.001). Disruptive behavior was reduced by 35% (p < 0.01), and adaptive functioning improved by 28% (p < 0.01). There was a 15% (p < 0.001) and 25% (p < 0.001) improvement in attendance and task completion, and academic performance, respectively, 12% (p < 0.01). There was an improvement in social adjustment (30% p < 0.001), peer interaction (22% p < 0.01), and emotional regulation (40% p < 0.001). Mediation analysis indicated that emotional regulation (β = −0.42, p < 0.01) and executive functioning (β = −0.38, p < 0.01) had a significant effect in reducing offending risk, which explained 58% of the variance. Specific, organized educational programs can considerably decrease the risk indicators of the behavioral risk factors through the empowerment of self-regulatory abilities. Interventions implemented at a young age can be used as prevention measures to reduce the risk of becoming an offender in the long term.