The project aims to elucidate the role of soil and plant microorganisms in enhancing wheat sustainability, nutritional quality, immunogenicity, and the composition of bioactive compounds in wheat plants. Two distinct case studies were implemented to examine the impact of agricultural practices (both ecological and conventional, including irrigation and non-irrigation conditions) as well as edaphoclimatic factors and wheat genetic varieties on soil and plant microbiota. The objective is to correlate these microbial communities and the soil-plant interactions with the nutritional, immunogenic, and bioactive composition of wheat, develop a bioinformatic tool to help select the wheat variety according to the proper edaphoclimatic conditions for specific nutritional outcome and select the microbes with best performance to design microbial-based food. Wheat samples from three harvesting campaigns were collected, and the characterization of soil and plant microbiota for both case studies are almost complete. Additionally, the analysis of the nutritional composition concerning the impact of agricultural practices is also mostly finalized. The fully assessment of the influence of edaphoclimatic and genetic conditions on nutritional composition is still ongoing. The quantification of total immunogenic proteins has been accomplished for both case studies, and the characterization of bioactive compounds is currently in progress. More than 30 fermented food prototypes (including beverages, and yogurt-type products) were developed by selecting the best microbial performance according to nutritional composition, bioactive compounds and food immunogenicity. To date, three wheat-based fermented beverages have already been selected and are now being scaled-up for sensory and clinical trials. All food prototypes are being analyzed in terms of bioactive compounds, gluten quantification and antinutritional and safety aspects for further research. In addition, WHEATBIOME has already defined the methodological procedure for assessing the environmental and economic performance of the project food prototypes. Survey questionnaires to food system actors were implemented in Hungary, Netherlands and Spain providing a widen evaluation on European food system's ability to provide healthy and sustainable food and feed, identifying barriers and enablers for adopting sustainable practices at the EU level, and determining the desired characteristics of novel wheat-based fermented food and feed products.