The effectiveness of multicomponent positive psychology interventions (MPPIs) on adolescents’ mental health has been studied with the use of standard procedures throughout the scientific literature. However, little is known about the potential mechanisms underlying the network structure of mental health following the dual-factor model after an MPPI. We relied on network analysis to explore the reorganization of the connections between mental health indicators after a school-based MPPI. Adolescents from two high schools in Spain were randomly allocated to the 6-week intervention group (n = 85) or to the control group (n = 135). Network analysis showed that the relations between the two differentiated network dimensions of mental health (i.e. well-being and psychological distress) changed after the intervention. Unlike control participants, emotional well-being was negatively associated with depression and stress, while psychological well-being was positively related to stress after the intervention. The present study supports the viability of the network approach in analyzing the connections between mental health indicators as defined by the dual-factor model and the contribution of MPPIs to change the complex pattern of relations between the dimensions of well-being and psychological distress.