Objective In response to the rise in mental health needs among youth, a school-based resilience intervention was implemented for sixth graders at an urban middle school. The goal of this analysis is to examine improvements in key mental health parameters among students who endorsed negative affectivity at baseline. Method A total of 285 11–12-year-olds (72% white, 18% Hispanic, 55% female) participated in a single-arm, non-randomized 6-week 1:1 school-based coaching intervention, Healthy Kids. Youth completed validated surveys at baseline and 6-week follow-up assessing depression/anxiety symptoms, bullying, self-efficacy, academic pressure, grit, and resilience. Participants were determined to have elevated negative affectivity if they reported mild-to-severe symptoms for both depression and anxiety symptoms. General linear models examined differences between groups for each mental health parameter, as well as change in outcomes from baseline to follow-up. Results A third of participants (38%) at baseline endorsed negative affectivity. Youth who endorsed negative affectivity were more often female (71% vs 29%; p < 0.001) and identified as victims of cyberbullying (25% vs 8%; p < 0.001). Youth with baseline negative affectivity scored lower for self-efficacy (total 70.5 vs 86.8; p < 0.0001). Baseline negative affectivity was a significant moderator for change in mental health parameters. Post-intervention, those who endorsed baseline negative affectivity, medium effect sizes were observed for self-efficacy ( g = 0.6; 95%CI 0.3, 0.9; p < 0.001) and anxiety symptoms ( g =  − 0.70; 95%CI − 1.0, − 0.4; p < 0.001). Among all youth, there were significant medium intervention effects in resilience ( g = 0.5; 95%CI 0.3, 0.7; p < 0.001) and self-efficacy ( g = 0.7; 95%CI 0.4, 0.9; p < 0.001). Conclusions A universal resiliency program may improve self-efficacy and symptoms of anxiety among youth experiencing negative affectivity, while improving resilience and self-efficacy among all youth. Our findings suggest a universal school-based coaching program benefits all youth, while also specifically targeting the needs of youth with negative affectivity who are most at risk for mental health concerns.