Abstract Background Effective interventions on screen-time behaviours (television, video games and computer time) are needed to prevent non-communicable diseases in low- and middle-income countries. The present manuscript investigates the effect of a school-based health promotion intervention on screen-time behaviour among 12- to 15-year-old adolescents. We report the effect of the trial on screen-time after two stages of implementation. Methods We performed a cluster-randomised pair matched trial in urban schools in Cuenca-Ecuador. Participants were adolescents of grade eight and nine (mean age 12.8 ± 0.8 years, n = 1370, control group n  = 684) from 20 schools (control group n  = 10). The intervention included an individual and environmental component tailored to the local context and resources. The first intervention stage focused on diet, physical activity and screen-time behaviour, while the second stage focused only on diet and physical activity. Screen-time behaviours, primary outcome, were assessed at baseline, after the first (18 months) and second stage (28 months). Mixed linear models were used to analyse the data. Results After the first stage (data from n  = 1224 adolescents; control group n  = 608), the intervention group had a lower increase in TV-time on a week day (β = −15.7 min; P  = 0.003) and weekend day (β = −18.9 min; P  = 0.005), in total screen-time on a weekday (β = −25.9 min; P  = 0.03) and in the proportion of adolescents that did not meet the screen-time recommendation (β = −4 percentage point; P  = 0.01), compared to the control group. After the second stage (data from n  = 1078 adolescents; control group n  = 531), the TV-time on a weekday (β = 13.1 min; P  = 0.02), and total screen-time on a weekday (β = 21.4 min; P  = 0.03) increased more in adolescents from the intervention group. No adverse effects were reported. Discussion and Conclusion A multicomponent school-based intervention was only able to mitigate the increase in adolescents’ television time and total screen-time after the first stage .