<p>At the crossroads between food studies and science and technology studies, this paper analyzes the role of laboratories located within traditional cheese territories in the ecologization of cheese microbiology in France at the turn of the twentieth century. The paper argues that their connectedness with Protected Designation of Origin raw-milk cheese organizations advocating for a strong understanding of terroir played a key role in challenging the modern strain-by-strain approach and fostering a shift towards a new research object: microbial communities in their ecologies. Modernization and standardization in cheese production from the 1950s onwards laid indeed on the improvement of hygiene to get “cleaner” milks, and on lab research on microbial strains to develop selected starter cultures. This led to a dramatic loss of microbial abundance within raw milks, which progressively provoked milk processing issues, as well as a loss of cheese typicality, an issue for place-based cheeses. To face it, the modernist approach promoted more laboratorial research on microbial strains to develop new starter cultures and the diversification of microbial collections, within an ex-situ conservation framework. In contrast, microbiologists conducting applied research for raw-milk terroir cheeses investigated environmental microbial reservoirs, microbial fluxes, as well as farming practices that favor “natural seeding” and enrich milk native microflora. A new approach emerged, namely “practice-driven microbial ecology” (<i>écologie microbienne dirigée</i>), which enacts the dynamic and ubiquitous properties of microbial life. The paper offers a situated account on the “microbial (ecology) turn” described by other authors, highlighting the ecological approach developed in the 1990s–2000s by French microbiologists in search of “the microbial path to terroir”.</p>