Wheat is a staple food in many diets and is currently cultivated worldwide. It provides a large proportion of the daily energy intake and contributes to food balance. Changes in agro-industrial practices in the bread sector, from the field to bread-making, have led to an increase in chronic diseases and nutritional deficits, emphasizing the link between food and health. Several levers could be used to improve the nutritional quality of bread wheat. Organic farming, by avoiding the use of pesticides, might allow for greater consumption of wholegrain products. Breeding wheat cultivars with an enhanced mineral content may serve as another lever. In this context, the on-farm participatory plant-breeding of highly diversified varieties could provide promising resources. This study investigated the sensory and nutritional quality of nine population varieties resulting from a ten-year participatory plant-breeding process compared to two commercial pure-line varieties. Analysis of variance showed genotype effects for Mg and Zn concentration, so breeding for a high Mg and Zn concentration can reasonably be envisaged. Moreover, a positive correlation was found between plant height, peduncle height (distance between the Last Leaf and Spike (LLSD)) and nutrient content. Finally, as population varieties express more differences in their profile when grown in less fertile soils, these results emphasize the benefits of genetic diversity for diverse nutritional intake and sensory properties.