In 2017, Köhler was appointed by António Guterres as his new special envoy for Western Sahara, in charge of restarting talks between Morocco and the Polisario independence movement over the disputed territory. In that capacity, Köhler invited the foreign ministers of Morocco, Algeria and Mauritania as well as the secretary general of the Polisario Front in late 2018 for a meeting in Geneva to broker a settlement over the territory; this marked the first time in six years that the involved parties met for negotiations. In 2019, he left his post on health grounds.