Background: Physical activity is a substantial promoter for health and well-being. Yet, while an increasing number of studies shows that the responsiveness to physical activity is highly individual, most studies focus this issue from only one perspective and neglect other contributing aspects. In reference to a biopsychosocial framework, the goal of our study is to examine how physically inactive individuals respond to two distinct standardized endurance trainings on various levels. Based on an assessment of activity- and health-related biographical experiences across the life course, our mixed-method study analyzes the responsiveness to physical activity in the form of a transdisciplinary approach, considering physiological, epigenetic, motivational, affective, and body image-related aspects. Methods: Participants are randomly assigned to two different training programs (High Intensity Interval Training vs. Moderate Intensity Continuous Training) for six weeks. After this first training period, participants switch training modes according to a two-period sequential-training-intervention (STI) design and train for another six weeks. In order to analyse baseline characteristics as well as acute and adaptive biopsychosocial responses, three extensive mixed-methods diagnostic blocks take place at the beginning (t0) of the study and after the first (t1) and the second (t2) training period resulting in a net follow-up time of 15 weeks. The study is divided into five modules in order to cover a wide array of perspectives. Discussion: The study’s transdisciplinary mixed-method design allows to interlace a multitude of subjective and objective data and therefore to draw an integrated picture of the biopsychosocial efficacy of two distinct physical activity programs. The results of our study can be expected to contribute to the development and design of individualised training programs for the promotion of physical activity. Trial registration: The study was retrospectively registered in the German Clinical Trials Register on 12 June 2019 (DRKS00017446).