The cheese microbial community is dense with relatively low complexity and composed of cultivable prokaryotic and eukaryotic microorganisms. The ripening process can thus be reproduced under controlled conditions. A reduced microbial community composed of yeasts and bacteria was assembled to mimic that of soft or semi-hard cheeses. The genomes of the microorganisms have been sequenced and annotated, which allows access to gene expression under various conditions at different ripening times. Through the use of a combined approach using omics (e.g. metatranscriptomics, volatilomics), and biochemical/microbial analyses, we have investigated the effect of various perturbations (biotic or abiotic) on the stability and functionality of the microbial cheese community. These perturbations are presented as case studies including: i) the effect of the omission of some yeast (e.g. D. hansenii or G. candidum), and, ii) the effect of increased sodium chloride content, on the functioning of the cheese ecosystem, iii) the effect of reduced sodium chloride combined with spoilage microorganisms (e.g. Pseudomonas, Yarrowia) supplementation on the stability of the microbial community in cheese produced in real technological conditions. Differential analyses of metatranscriptomic data showed the resilience of the communities’ functions when submitted to disturbance. Multivariate integrative analysis of metatranscriptomic data and volatile compounds data resulted in the identification of key metabolic pathways correlated to the production of volatile compounds. Approaches such as those presented above require methodological choices for the standardization and integration of heterogeneous data. These methods are useful in functional ecology prospects to give a view of the function and resilience of cheese communities and open perspectives in the design/formulation of microbial communities with target functions, including sensorial and/or health benefits.