Restoring natural grasslands alters the soil microbiome and biogeochemical processes, particularly carbon (C) and nitrogen (N) cycling. One of the primary ways to restore degraded grasslands is to restrict grazing for a period so that the ecosystem can recover. We examined the relationship between changes in soil microbiome composition and function with greenhouse gas emissions and soil properties during the restoration of a semiarid steppe in China. Grazing exclusion for 15 years increased CO2 and N2O emissions and CH4 uptake compared with those for 6 or 37 years. A 15- and 37-year grazing exclusion led to higher soil organic carbon levels, which correlated with increased bacterial populations and genes associated with the decomposition of carbon-rich substrates and elevated CO2 emissions. After 15 years of grazing exclusion, the abundance of methanotrophic microbes was higher, and the abundance of methanogenic microbes was lower, increasing CH4 uptake compared to continuous grazing (the control). Compared to the control (continuous grazing), 15 years of grazing exclusion resulted in elevated methanotrophic populations, depressed methanogenic populations, and consequently, enhanced CH4 uptake. Emissions of N2O increased with following increases in denitrification genes norB. Structural equation modeling revealed that grazing exclusion's effects on CO2, N2O, and CH4 fluxes were mediated by changes in plant community characteristics, soil fertility, and soil microbiomes. Further research on the microbial drivers of recovery could lead to improved management practices and ecosystem restoration and resilience.