The interest in Nature-based Interventions as ways to improve human wellbeing and health has rapidly increased in recent years. However, there is still limited evidence on which ecosystem properties trigger specific beneficial psycho-physical effects. Here we present the results of a pilot study conducted in a woodland ecosystem in central Italy, where a nine-month “Green Prescription” programme for patients with chronic health conditions was developed and implemented by a medical doctor within an ecological-enactive approach, in which participants actively engaged with the woodland while learning to respect its ecological constraints. To characterize the ecological properties of the woodland, we developed an Ecosystem Structural Complexity Index, which integrates vegetation cover, vertical stratification, and biodiversity metrics as a synthetic measure of the structural complexity of the woodland patches where the intervention took place. Our analysis found significant associations between ecosystem structural complexity and participant responses. In particular, woodland patches characterized by higher structural complexity consistently elicited overall appreciation, greater levels of self-reported relaxation, and physical symptoms relief compared with structurally simpler patches. Moreover, the observed benefits appeared to accumulate over time, with distinct temporal patterns suggesting that dynamics and fluctuations in ecological functions may influence human responses. The results support the hypothesis that ecosystem structure may play an important role in shaping the health-supporting potential of the natural environment, and highlight the importance of integrating ecological assessments, achieved by ecologists and trained professionals, into the planning, design, and evaluation of Nature-based Interventions and Green Prescriptions. We argue that Green Prescriptions, when ecologically designed, may support both human health and ecosystem integrity, in line with the Planetary Health perspective. More broadly, these findings provide futher evidence that conserving ecosystem complexity and ecological integrity is important not only for biodiversity conservation, but also for maintaining the capacity of ecosystems to support human health and wellbeing.