Northern ecosystem processes play out across scales that are rare elsewhere on contemporary earth: large ranging predator–prey systems are still operational, invasive species are rare, and large-scale natural disturbances occur extensively. Disturbances in the far north affect huge areas of land and are difficult to control or manage. Historically, disturbance patterns and processes ranging across a number of spatio-temporal scales have played an important role in the resilience of northern ecosystems. However, due to interactions with a warming climate, these disturbances are now erasing key legacies of the last millennia of ecosystem processes. Building on the concepts of legacies and cross-scale interactions, we highlight several general conceptual issues that represent key challenges for the future of northern ecosystem science, but that also have relevance to other biomes.