Stabilizing ecosystems is a great challenge, explained by their high degree of biodiversity. Each microorganism composing the ecosystem exhibits distinct resistance to preservation processes. The association specificity depends on the maintenance of the function and population level for each microorganism of the ecosystem after stabilization. This dataset comprises experimental data related to the response of each microorganism of a cheese ecosystem at two maturation steps (fresh and after 22 days of ripening), to stabilization and storage. A simplified microbial ecosystem (10 microorganisms and 9 species) was preserved directly in the cheese using freezing and freeze-drying. Such processes are conventionally employed to stabilize starters. The microorganisms' culturability (plate counts) was quantified after freezing, freeze-drying, and one month of storage at different temperatures. The physical characterization of the matrix by differential scanning calorimetry (glass transition temperature of frozen samples and thermal events taking place in freeze-dried samples) was performed to get an insight into the preservation mechanisms.