Abstract Background Behaviour change interventions targeting physical activity, diet, sleep and sedentary behaviour of teenagers show promise when delivered through smartphones. However, to date there is no evidence of effectiveness of multicomponent smartphone-based interventions. Utilising a user-centred design approach, we developed a theory-based, multi-dimensional system, PEGASO Fit For Future (PEGASO F4F), which exploits sophisticated game mechanics involving smartphone applications, a smartphone game and activity sensors to motivate teenagers to take an active role in adopting and maintaining a healthy lifestyle. This paper describes the study protocol to assess the feasibility, usability and effectiveness (knowledge/awareness and behavioural change in lifestyle) of the PEGASO system. Methods We are conducting a quasi-experimental controlled cluster trial in 4 sites in Spain, Italy, and UK (England, Scotland) over 6 months. We plan to recruit 525, in a 2:1 basis, teenagers aged 13–16 years from secondary schools. The intervention group is provided with the PEGASO system whereas the comparison group continues their usual educational routine. Outcomes include feasibility, acceptance, and usability of the PEGASO system as well as between and within group changes in motivation, self-reported diet, physical activity, sedentary and sleeping behaviour, anthropometric measures and knowledge about a healthy lifestyle. Discussion PEGASO F4F will provide evidence into the cross-cultural similarities and differences in the feasibility, acceptability and usability of a multi-dimensional smartphone based behaviour change intervention for teenagers. The study will explore facilitating factors, challenges and barriers of engaging teenagers to adapt and maintain a healthy lifestyle when using smartphone technology. Positive results from this ICT based multi component intervention may have significant implications both at clinical level, improving teenagers health and at public health level since it can present an influential tool against the development of chronic disease during adulthood. Trial registration https://clinicaltrials.gov Registration number: NCT02930148, registered 4 October 2016.