The invaders established a new ruling class, the arma, who after 1612 became virtually independent of Morocco. However, the golden age of the city was over and it entered a long period of decline. Different tribes governed until the French took over in 1893, a situation that lasted until it became part of the current Republic of Mali in 1960. Presently, Timbuktu is impoverished and suffers from desertification.

In its Golden Age, the town's numerous Islamic scholars and extensive trading network made possible an important book trade: together with the campuses of the Sankore Madrasah, an Islamic university, this established Timbuktu as a scholarly centre in Africa. Several notable historic writers, such as Shabeni and Leo Africanus, have described Timbuktu. These stories fueled speculation in Europe, where the city's reputation shifted from being extremely rich to being mysterious. This reputation overshadows the town itself in modern times, to the point where it is best known in Western culture as an expression for a distant or outlandish place.