Background Several phenomena may point to potentially detrimental cardiac effects of endurance exercise, such as elevated circulating cardiac troponin levels and reductions in systolic and diastolic function directly after marathon completion. Furthermore, while myocardial abnormalities have been reported in patients who recovered from COVID-19, the cardiac impact of extensive endurance exercise in individuals who recovered from COVID-19 remains unknown. We therefore aim to investigate (potentially detrimental) cardiac effects of first-time marathon training and participation, including a subset of participants who recovered from COVID-19, in apparently healthy middle-aged men. Study design This exploratory prospective cohort study investigates cardiac effects of first-time marathon running in 24 middle-aged (35–50 years) healthy men. Primary outcomes are cardiac morphological changes from pre-training up to 1 month after marathon completion, measured with magnetic resonance imaging (MRI) at 4 time points: 1) baseline (4 months before the marathon), 2) pre-marathon (2 weeks before the marathon), 3) post-marathon (< 24 h post-marathon), and 4) recovery (4 weeks after the marathon). Secondary parameters include other cardiac or non-cardiac changes: 1) quantitative MRI myocardial mapping, including mean diffusivity and extracellular volume fraction, 2) echocardiographic morphology and function changes, 3) VO2max, 4) electrocardiogram changes, and 5) levels of cardiac biomarkers. Discussion This study will contribute to our understanding of cardiac adaptations and maladaptations to first-time marathon running in middle-aged men, and the interaction between extreme endurance exercise and potential detrimental cardiac effects, also in the context of COVID-19. Results will inform on future research directions while providing new clinical insights for health professionals involved in athlete care.