Cedrus atlantica (Atlas cedar) is a relict and endemic endangered species from northwestern African mountains, whose distribution range has undergone a dramatic reduction over recent decades. Long-term studies are needed for a better understanding of the development of its range as well as for assisting in the implementation of sustainable conservation measures. The multi-proxy analysis of a high-resolution fossil record of 180 cm depth allowed us to depict the final demise of an Atlas cedar population from the western Rif Mountains (Jbel Khesana), despite its high resilience during the last ~4000 years. Currently, Atlas cedar trees are not observed in Jbel Khesana but they still occur in the nearby area as scattered populations on a few mountain tops at altitudes higher than 1400 m a.s.l. Our data show an initial relatively stable period (~4000–2400 cal. yr BP) followed by a phase where both climatic and human-induced disturbances cause an alternate dominance of oaks and Atlas cedars (2400~1550 cal. yr BP). Then, the increasing aridity and human activities favoured the depletion of Atlas cedar forests (~1550–800 cal. yr BP). Our record shows that Atlas cedar forests have recovered after each deforestation event, which reveals a high resilience of the species until the mid-20th century, when they became extinct in the study area. The main driver of their local extinction may be attributed to the strong human pressure. Management measures of Atlas cedar in the Rif Mountains should aim at limiting intensive loggings and protecting the existing populations for their local regeneration.