Background: The COVID-19 pandemic has exacerbated the already existing pandemic of physical inactivity. In adolescents, the effect of COVID-19 related governmental measures may be even more pronounced, as they experience school closures, home confinement, social distancing and possible mental health issues as a result. The current study uses the COVID-19 pandemic and associated governmental measures as a natural experiment to understand the impact on the lifestyle of adolescents with relation to physical activity, sedentary and dietary behaviour. We also aim to describe the determinants of change in lifestyle behaviours. Methods/Design: A before-after experimental study design will be followed in which baseline measurements have been undertaken in 2018-19 before the COVID-19 pandemic, and the follow-up measurements will be repeated during the COVID-19 pandemic. Twenty schools of Punjab, India form the primary unit of participation from which 1086 adolescents participated in the study. Validated questionnaires are used to measure physical activity, sedentary behaviour, and dietary behaviour. Additionally, objective measures of physical activity will be performed using accelerometer over a 7-day period on a sub-sample. Body mass index (BMI) and waist circumference will be assessed objectively as a measure of central obesity. Qualitative interviews and focus group discussions will be conducted to have a better understanding for reasons of change in physical activity, sedentary and dietary behaviour or any possible differences between groups. Discussion: The study aims to reveal the impact of COVID-19 related governmental measures on physical activity, sedentary and dietary behaviour of adolescents. It is one of the first studies to show both subjective and objective measures of physical activity levels and sedentary time of school-going adolescents during COVID-19. Due to the mixed method approach we will be able to identify reasons for changes in lifestyle behaviours and possibly find innovative ways of staying physically active during the era of physical distancing.