Kobresia pygmaea pastures on the Tibetan Plateau face destruction while storing 2.5% of the global soil organic carbon (SOC). Representative soil samples were taken from soils of six successional degradation stages (S0 – S5) at Nagqu close to the KEMA research station on the Tibetan Plateau at 4,484 m a.s.l. in late summer 2013 and 2015. SOC stocks decrease from intact pastures (S0) to severely degraded stages (S5) by 70%. The dataset indicates SOC and nitrogen (N) losses but also includes changes in their isotopic composition. Furthermore, pH, CEC, element contents and the lignin monomers (vannillyl, syringyl, and cinnamyl (VSC) were quantified and point towards a change of soil properties. These changes affect the microbial community structure of bacteria and fungi analyzed via terminal restriction fragment length polymorphism analysis (t-RFLP). Illumina MiSeq sequencing data of the microbial community are available under the project number PRJNA626504 at the NCBI. Functional implications of these shifts in microbial community structure were assessed by identifying pronounced alterations in enzyme activities for β-glucosidase, xylanase, urease, alkaline phosphatase and phenol oxidase. Structural and functional shifts as adaption to SOC losses define a “tipping point” where the magnitude of changes in the soil-microbiome interaction of one of the world's largest grassland ecosystem exceeds a threshold that not only alters this system permanently, but which also diminishes its function as CO2-sink triggering cascading climate effects up to the global scale.