Widespread changes to near-surface permafrost in northern ecosystems are occurring through top-down thaw of near-surface permafrost and more abrupt localized thermokarst. Both types of thaw are associated with a loss of ecosystem services, including soil hydrothermal and mechanical stability and long-term carbon storage. Here, we analyze relationships between ground layer vegetation, active layer thickness, and greenhouse gas fluxes along a thaw gradient from permafrost peat plateau to thaw bog in Interior Alaska. We used active layer thickness to define four distinct stages of thaw: Stable, Early, Intermediate, and Advanced, and we identified key plant taxa that serve as reliable indicators of each stage. Advanced thaw, with a thicker active layer and thermokarst, was associated with increased abundance of graminoids and Sphagnum mosses but decreased plant species richness and ericoid abundance. Early thaw, driven by active layer thickening with little visible evidence of thermokarst, coincided with a fivefold increase in CH4 emissions, accounting for ~30% of the total increase in methane emissions occurring in ~10% of the timeline of the forest-to-bog transition. Our findings suggest that early stages of thaw, prior to the formation of thermokarst features, are associated with distinct vegetation and soil moisture changes that lead to abrupt increases in methane emissions, which then are perpetuated through ground collapse and collapse scar bog formation. Current modeling of permafrost peatlands will underestimate carbon emissions from thawing permafrost unless these linkages between plant community, nonlinear active layer dynamics, and carbon fluxes of emerging thaw features are integrated into modeling frameworks.