Previous scientific research on the use of mobile applications to increase physical activity level and improve health among adolescents does not provide conclusive results, one of the main reasons being the lack of adherence to the intervention after the first weeks. For this reason, the main objectives of the research were to determine the changes produced by a compulsory ten-week period of after-school intervention with mobile step-tracking applications on adolescents' health; and the final objective to compare the benefits obtained by each of the mobile applications. To meet the objectives, a longitudinal study with non-probability convenience sampling was proposed. The sample consisted of 400 adolescents from two public compulsory secondary schools in the Region of Murcia, Spain, whose body composition, level of physical activity, adherence to the Mediterranean diet, and physical fitness were measured. The SPSS statistical software was used for statistical analysis. The results showed that adolescents in the experimental group showed a higher level of physical activity and better body composition and physical fitness variables after the intervention compared to the control group, with differences between the different applications used. In conclusion, this research shows the usefulness of mobile applications if they are used in a compulsory way after school hours. The relevance of these results for policymakers lies in the fact that they provide statistical data on the usefulness of mobile applications as an educational resource, being an option to make up for the lack of sufficient physical education teaching hours to meet global physical activity recommendations.