The increasing prevalence of unhealthy lifestyle choices contribute to almost all chronic conditions negatively affecting individual and public health. As the most beneficial preventative solution, a healthy lifestyle focusing on the dual approach of physical activity (PA) and a healthful diet is highly recommended. Considering the growing number of people interested in sustainable, plant-based diets, it seems crucial to analyze lifestyle behaviors with a special focus on diet type to delve deeper into the unenthusiastic health status among young populations. Therefore, this multidisciplinary study aims to survey and scale health behaviors with a special focus on the prevalence of traditional and vegetarian diets in connection with PA levels among Austrian pupils (10–19 years), teachers and principals in secondary education levels I and II. Following a cross-sectional design, sociodemographic and school-related data along with a complete profile of lifestyle behaviors, including detailed information regarding diet, PA, sports & exercise, and other health-related behaviors, were collected using online-based questionnaires. A total number of 8,845 children/adolescents (~1.2% of the eligible 771,525 Austrian secondary school pupils) and 1,350 adults (~1.5% of total eligible 89,243 Austrian teachers/principals) participated in the study. As this is the first investigation to explore the prevalence of veganism/vegetarianism amongst a large group of pupils, the present study will add an important contribution to overcome the lack of knowledge on PA, sports & exercise linked to healthy alternative diets. With a sustainable healthy lifestyle, a healthy transition from childhood to adulthood occurs, which can result in growing healthier functioning generations at all social levels. As a study protocol, the present article is intended to present comprehensive details of the study design, objectives, and the associated analytical procedures of the “From Science 2 School” study.