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In a context of climate change, agro-ecological practices offer possible solutions to strengthen food agricultural systems. These practices are particularly significant for farms producing raw milk cheeses, in which they influence a great diversity of holobionts and environmental microbiota from the soil to the product. The TANDEM project aims to contribute to a better understanding of how microorganisms in the dairy food chain respond to changes associated with an agro-ecological transition. Our strategy will be i/ to compare agro-ecological vs intensive farming systems and to study their responses to disturbance and ii/ to reassess the knowledge on microbial transfers in a field context and with regard to the diversity of connections between human beings and microbes in the dairy system. TANDEM brings together a multidisciplinary consortium combining agronomy, ecology, microbiology, animal and food sciences, bioinformatics, biostatistics and sociology, and associating key stake-holders in the cheese sector. The originality of the project lies in i/ the advanced characterization of microbial transfers for an integrative approach of all microbiota at the intra-species and functional scales, ii/ identifying microbial indicators along the food chain to evaluate the impact of changes in practices, iii/ deploying new concepts associated with the contribution of living beings in these systems. TANDEM offers perspectives for better managing food systems transitions, contributing to the three pillars of sustainability and to global health.