This empire, though almost as large as that of the Sokoto Fulani to the east, was by no means so soundly based. Whatever 'Umar's original motives may have been, his followers seem to have been as much concerned with amassing riches and power as with converting their subjects to Islam. Numerous risings against Tukulor authority by the conquered Bambara and Fulani continually shook the empire, and in 1864 'Umar himself was killed. His son and successor, Ahmadu Seku, inherited a patrimony disturbed by inner conflicts and rival claims to power. For the sake of internal order, in the 1880s he began to disband his army and put increasing reliance on the loyalty of subject peoples. The policy failed; not only did Ahmadu fail to win new loyalties, but he lost the adherence of the Tukulor themselves as they saw their privileged position erode. The French exploited the situation by constructing forts within Tukulor territory and signing treaties of friendship with Tukulor's neighbours. After 1890, French troops swept the empire, conquering Segu, Macina, and Timbuktu in turn. Ahmadu succumbed to the French in 1893, and his former empire was soon firmly incorporated into French overseas territory.

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After 'Umar was killed in a skirmish with the Fulani in 1864, his vast domains were divided among his sons and commanders. His eldest son, Amadou Tal, who had been installed at Ségou, unsuccessfully attempted to exert control over the whole Tukulor empire in a series of civil wars. He became head of the Ségou Tukulor empire, whose predominantly Bambara inhabitants led constant revolts against his rule.

The French, who established a fort at Médine in western Mali in 1855, viewed the Ségou Tukulor empire as the principal obstacle to their acquisition of the Niger River valley. Fearful of British designs on the same region, they engaged in a series of diplomatic overtures and military operations to push the boundaries of their control eastward. Between 1880 and 1881 the French succeeded in expanding their control from Médine 200 miles east to Kita, primarily through the diplomatic efforts of Captain Joseph-Simon Gallieni, who signed protectorate treaties with chiefs at Bafoulabé and Kita.

In 1883 Gustave Borgnis-Desbordes launched a series of military campaigns against the Tukulor and the forces of Samory Touré, a Dyula Muslim leader who founded a state to the south. Desbordes captured Bamako during that year, giving the French a presence on the Niger. Between 1890 and 1893, Colonel Louis Archinard launched a series of successful military operations that led to the final conquest of Ségou in 1893. Samory, who was driven into the Ivory Coast, was captured in 1898, the same year that the small Dyula kingdom of Kenedougou around Sikasso was conquered by French forces under Colonel H.M. Audeod. Timbuktu was conquered in 1894 by the French officers Gaston Boiteaux, Eugène Bonnier, and Joseph-Jacques Joffre, and the southern Sahara was finally pacified by méharistes (camel corps) by 1899.