The effectiveness and program mechanisms of a whole-school anti-bullying program that builds on the socio-ecological framework were investigated by applying person-oriented methods of data analyses. A longitudinal cluster randomized control study was utilized comprising 1377 adolescents (48.5% girls, M[subscript age] = 11.7) who participated in a 1-year whole school anti-bullying program that was implemented in 13 schools and 665 adolescents (45.2% girls, M[subscript age] = 11.6) who attended 5 control schools. Student reports were collected at pre- and post-test within a 1-year interval. Applying latent profile analyses (LPA), students who were actively involved in bullying as perpetrators (e.g., bullies), who were the target of bullying (e.g., victims), who were both (e.g., bully-victims), and who were not involved either as perpetrators or victims (e.g., uninvolved) were identified. Latent transition analyses (LTA) investigated transition patterns between bully, victim, bully-victim, and uninvolved subgroups in the control and intervention group before and after the 1-year program implementation. Program effectiveness (e.g., a higher transition probability in the intervention compared to the control group) were found for victims and bully-victims. It was explored whether changes in program mechanisms were differently related to changes in these sub-group memberships in the intervention group. Victims transiting to the uninvolved sub-group increased in help-seeking and anti-bullying norms, while bully-victims transiting to the uninvolved sub-group increased help-seeking, perceived teacher intervention, and anti-bullying norms. It can be concluded that this program works differently for different sub-groups of students and that different mechanisms of change drive changes in different sub-groups of students.