There is increasing interest in food system’s microbiomes. Microbiomes are highly important to achieve sustainable primary production, to increase food quality and safety, to maintain food production and ultimately, they are of key relevance for human and animal health. In this conference we will discuss the role of food system’s microbiomes for burning issues like the fertilizer crisis, animal welfare, antibiotic resistance, food quality, circularity and dietary transition. We aim to further increase the awareness of food system microbiomes across different stakeholder groups!