Diets, but also overall food environments, comprise a variety of significant factors with direct and indirect impacts on human health. Eco-Regions are geographical areas with a territorial approach to rural development, utilizing organic food and farming practices, and principles and promoting sustainable communities and food systems. However, so far, little attention has been given to quantifying aspects of the health of citizens living in these sustainable transition territories. The project "Indicators for Assessment of Health Effects of Consumption of Sustainable, Organic School Meals in Eco-Regions" (INSUM) aims to identify and discuss research approaches and indicators that could be applied to effectively measure the somatic, mental, and social health dimensions of citizens in Eco-Regions, linked to the intake of organic foods in their diets. In this paper, we focus on the somatic (physical) health dimension. A two-day workshop was held to discuss suitable methodology with an interdisciplinary, international group of experts. The results showed the limitations of commonly used tools for measuring dietary intake (e.g., relying on the memory of participants), and nutritional biomarkers (e.g., variations in correlations with specific intakes) for research understanding dietary intake and the health effects of diets. To investigate the complexity of this issue, the most suitable approach seems to be the combination of traditional markers of physical and mental health alongside emerging indicators such as the microbiome, nutrigenomics, metabolomics, or inflammatory biomarkers. Using new, digital, non-invasive, and wearable technologies to monitor indicators could complement future research. We conclude that future studies should adopt systemic, multidisciplinary approaches by combining not only indicators of somatic and mental health and social wellbeing (MHSW) but also considering the potential benefits of organic diets for health as well as aspects of sustainability connected to food environments.