Climate change has irrevocable consequences for the otherwise well-preserved archaeological deposits in the Arctic. Vegetation changes are expected to impact archaeological sites, but currently the effects are poorly understood. In this article we investigate five archaeological sites and the surrounding natural areas along a climate gradient in Southwest Greenland in terms of vegetation types, above- and below-ground biomass, soil geochemistry and spectral properties. The investigations are based on data from site-sampling and optical remote sensing from an unmanned aerial vehicle (UAV) and satellites. Results show that the archaeological sites are dominated by graminoids with approximately two times more above- and below-ground biomass than the surrounding areas, where the vegetation is more heterogeneous. This difference is associated with a 2–6 times higher content of plant available phosphorus and water extractable nitrate and ammonium in the archaeological deposits compared to the surrounding soil. Furthermore, the vegetation at archaeological sites is less affected by the regional climate variations than the surrounding natural areas. This suggests that soil-vegetation interactions at archaeological sites are markedly different from the natural environment. Thus, the long-term vulnerability of buried archaeological remains cannot be assessed based on existing projections of Arctic vegetation change. Finally, the study demonstrates that vegetation within archaeological sites has distinct spectral properties, and there is a great potential for using satellite imagery for large scale vegetation monitoring of archaeological sites and for archaeological prospection in the Arctic.