Permafrost formation and degradation creates a highly patchy mosaic of boreal peatland ecosystems in Alaska driven by climate, fire, and ecological changes. To assess the biophysical factors affecting permafrost dynamics, we monitored permafrost and ecological conditions in central Alaska from 2005 to 2021 by measuring weather, land cover, topography, thaw depths, hydrology, soil properties, soil thermal regimes, and vegetation cover between burned (1990 fire) and unburned terrain. Climate data show large variations among years with occasional, extremely warm–wet summers and cold–snowless winters that affect permafrost stability. Microtopography and thaw depth surveys revealed both permafrost degradation and aggradation. Thaw depths were deeper in post-fire scrub compared to unburned black spruce and increased moderately during the last year, but analysis of historical imagery (1954–2019) revealed no increase in thermokarst rates due to fire. Recent permafrost formation was observed in older bogs due to an extremely cold–snowless winter in 2007. Soil sampling found peat extended to depths of 1.5–2.8 m with basal radiocarbon dates of ~5–7 ka bp, newly accumulating post-thermokarst peat, and evidence of repeated episodes of permafrost formation and degradation. Soil surface temperatures in post-fire scrub bogs were ~1 °C warmer than in undisturbed black spruce bogs, and thermokarst bogs and lakes were 3–5 °C warmer than black spruce bogs. Vegetation showed modest change after fire and large transformations after thermokarst. We conclude that extreme seasonal weather, ecological succession, fire, and a legacy of earlier geomorphic processes all affect the repeated formation and degradation of permafrost, and thus create a highly patchy mosaic of ecotypes resulting from widely varying ecological trajectories within boreal peatland ecosystems.