There is little evidence regarding the effect mechanisms of social-emotional learning programs on children's peer relationships. The current study evaluated a novel school-based social-emotional learning program for the first year of secondary school assessing effects on social-emotional skills, peer connectedness, happiness, student and teacher classroom climate. The sample included 19 intervention classrooms (n = 399) and 16 waitlist-control classrooms (n = 281), with a mean age of 10.34 (SD = 0.76) and 48.8% girls. The main intervention effect analysis followed a per-protocol approach and was thus conducted with eight classes that finished all sessions (n = 195) and the control group classes (n = 281). It was further hypothesized that increases in social-emotional skills would predict peer connectedness and class climate increases, which would predict happiness. Results indicated significant intervention effects for social skills, peer connectedness and happiness. Classroom climate declined for both groups, seemingly affected by the school transition. Hypothesized relationships between target variables were partly supported with significant effects of social-emotional skills on connectedness and significant effects of peer connectedness on happiness for children reporting connectedness decreases. Additional analyses were conducted including all classrooms to compare the intervention's effectiveness across different implementation progress groups. Significant group differences were found, indicating that implementation aspects impact intervention outcomes. The findings indicate that universal, school-based social-emotional leaning programs are effective approaches to support peer relationships in the context of the school transition. However, more implementation support seems to be needed to ensure best-practice delivery and achieve maximal intervention effectiveness.