Marathon running is an increasingly popular form of physical activity. Despite its popularity, sport psychology research on marathon runners is limited, as are interdisciplinary approaches to evaluating performance results and health consequences of marathon training. Our Sports Medicine Psychology Laboratory research group partnered with exercise physiologists from the Sports Performance Laboratory 3 years ago to implement an ongoing interdisciplinary research program examining physical and psychological adaptations among approximately 100 novice runners taking a university-sponsored course in marathon training. Each year we have employed a repeated-measures design and made adaptations to the psychological constructs measured based on a specific overall purpose and focus for that year. We employed quantitative methods of analysis following the first and second years’ data collections to assess physical and psychological factors predicting sport injuries and psychological responses to injuries and in the third year to examine positive psychology constructs related to participation and performance. In this case study, we describe the methods of the sport psychology component of this marathon training study as well as the challenges and lessons learned while conducting this research.