In 1852 he was transferred to Senegal as deputy director of engineers and soon impressed the local merchant community as a capable and energetic administrator. Two years later, he was promoted to the rank of major and appointed governor of Senegal.

As governor, Faidherbe was alarmed by the growing power of the militant Islamic leader 'Umar Tal on the frontiers of Senegal. Abandoning the cautious policies of his predecessors, Faidherbe took the offensive against all those who threatened French primacy. In a series of well-executed campaigns, some undertaken against the wishes of the French government, he subjugated the Moorish tribes in the north, drove the forces of 'Umar Tal off the lower Sénégal River, and extended French control southward toward the Gambia. By 1861 he had transformed his colony from a collection of scattered trading posts into the dominant political and military power in this region of West Africa.

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In 1854, at the request of local merchants, Napoleon III appointed as governor Commandant Louis-Léon-César Faidherbe, who began to establish French military hegemony. He soon came into conflict with al-Hajj 'Umar, a Tukulor from Fouta-Toro who, having become regional head of the Tijaniyah fraternity, was establishing an economic and military power base in the upper Niger Valley; but a military stalemate after 1857 led to a truce of coexistence. When Faidherbe retired in 1865, French power was paramount over most of the territory of modern Senegal; and growing exports of peanuts, through the new colonial port of Dakar, were providing some economic resources.