Remains from Paleo-Eskimo cultures are well-documented, but complete preservation is rare. Two kitchen middens in Greenland are known to hold extremely well-preserved organic artefacts. Here, we assess the fate of the Qajaa site in Western Greenland under future climate conditions based on site characteristics measured in situ and from permafrost cores. Measurements of thermal properties, heat generation, oxygen consumption and CO2 production show that the kitchen midden can be characterized as peat but produces 4–7 times more heat than natural sediment. An analytical model from permafrost research has been applied to assess future thawing of the midden. Results show that the preservation conditions are controlled by freezing temperatures and a high water/ice content limiting the subsurface oxygen availability. Threats to the future preservation are related to thawing followed by drainage and increasing subsurface oxygen availability and heat generation. The model predicts that the unique 4000-year-old Saqqaq layer below more than 1 m of peat is adequately protected against thawing for the next 70 years.