To educate the relational well-being in order to learn to live together in society is one of the main needs of modern physical education (PE). Teachers are in need of pedagogical models to instruct peaceful coexistence and transform possible conflicts into PE. The goal of this study was to determine the effect of a pedagogical model (GIAM model) designed for conflict transformation on the relational well-being of students in obligatory secondary school (ESO in Spain). This study was an empirical research (associative strategy, comparative study using mixed methods). A number of 287 valid students (M = 14.90; SD = 0.66) participated in this study from 4 different secondary schools (SSs): third ESO (SS1 (n = 75); SS3 (n = 45); SS4 (n = 86)) and fourth ESO (SS2 (n = 81)). A sequence of seven learning sessions was conducted, the intervention of the teachers on the GIAM model and the student’s motivational climate perception caused by this learning sequence was analyzed. The teachers who best adapted their intervention to the GIAM model obtained greater significant changes (p < 0.005) in favor of the relational well-being of their students. This research provides scientific evidence and intervention strategies for students to learn how to transform the conflicts, adopting a collaborating style based on reflection-for, -in- and on-motor action.