BACKGROUND: To date, few mobile health (mHealth) interventions aimed at changing lifestyle behaviors have measured long term effectiveness. At the 6-month follow-up the MINISTOP trial found a statistically significant intervention effect for a composite score comprised of fat mass index (FMI) as well as dietary and physical activity variables; however, no intervention effect was observed for FMI. Therefore, the aim of this study was to investigate if the MINISTOP intervention 12-months after baseline measurements: (i) improved FMI and (ii) had a maintained effect on a composite score comprised of FMI and dietary and physical activity variables. METHODS: A two-arm parallel randomized controlled trial was conducted in 315 healthy 4.5 year old children between January 2014 and October 2015. Parents' of the participating children either received the MINISTOP intervention or a basic pamphlet on dietary and physical activity behaviors (control group). After 6 months, participants did not have access to the intervention content and were measured again 6 months later (i.e. the 12-month follow-up). The Wilcoxon rank-sum test was then used to examine differences between the groups. RESULTS: At the 12-month follow-up, no statistically significant difference was observed between the intervention and control groups for FMI (p = 0.57) and no maintained effect for the change in composite score was observed (mean ± standard deviation for the intervention and control group: + 0.53 ± 1.49 units and + 0.35 ± 1.27 units respectively, p = 0.25 between groups). CONCLUSIONS: The intervention effect observed at the 6-month follow-up on the composite score was not maintained at the 12-month follow-up, with no effect on FMI being observed at either follow-up. Future studies using mHealth are needed to investigate how changes in obesity related markers in young children can be maintained over longer time periods. TRIAL REGISTRATION: ClinicalTrials.gov ( NCT02021786 ; 20 Dec 2013).