High-latitude regions store large amounts of carbon trapped by ice sheets, permafrost and gas hydrates, yet joint evolution of these climate components is poorly understood. Covered by a cold-based ice-sheet during the last glaciation, the seafloor of the northeastern Barents Sea reveals one of the largest known glacitectonic provinces in the Arctic. Up to 200-m high glacitectonic landforms are cratered and overlie faults associated with ‘bright spots’ indicative of subsurface gas accumulations. However, sediment samples show low pore gas concentrations and no present-day gas seepage. We combine new observations and ice-sheet - hydrate modelling to propose that during the Late Weichselian, glacitectonism was caused by patchy substrate stiffening due to gradual growth of subglacial gas hydrates and permafrost. Ice decay led to rapid destabilisation and full drainage of shallow hydrate reservoirs and permafrost thaw, causing craterisation which was likely accompanied by large fluxes of carbon released into the water column. This study shows that these processes were more widespread across glaciated margins, also highlighting sensitivity and potential for abrupt changes of high-latitude carbon pools in response to complex interactions between the cryosphere, ocean, and solid earth.