In 1852 he was transferred to Senegal as sub-director of engineers, and in 1854 was promoted chef de bataillon and appointed governor of the colony on December 16. He held this post with one brief interval (1861 – 1863) until July 1865.

The work he accomplished in West Africa constitutes his most enduring legacy. At that time France possessed in Senegal little else than the town of Saint - Louis and a strip of coast. Explorers had, however, made known the riches and possibilities of the Niger regions, and Faidherbe formed the design of adding those countries to the French dominions. He even dreamed of creating a French African empire stretching from Senegal to the Red Sea.

Faidherbe's primary legacy was the means by which French colonialism expanded. Under the French Second Empire, the ideology of opening foreign markets to Free Trade came to dominate metropolitan interests in West Africa. In practice this meant free access by French interests to African markets and resources, in which conditions, prices, and products to be produced by Africans were enforced by European coercion. Since the 18th century, attempts to circumvent the traditional African controlled and taxed trade routes into the interior met with little success. Faidherbe, under the justification of extending security for Europeans, made the French military the engine of expansion.

Faidherbe's actions were not of his own creation, but were an implementation of "The Plan of 1854": a series of ministerial orders given to Governor Protet that originated in petitions from the powerful Bourdeaux based Maurel and Prom company, the largest shipping interest in St. Louis. The plan specified in detail the creation of forts along the Senegal river to end African control of the acacia gum trade from the interior. Faidherbe's push to build fortifications farther out, his conflicts with Protet, and his protests to Paris over Protet's inaction earned him the governorship in 1854.

Within three months of his appointment as Governor, he had begun work on the first in a series on inland forts up the Senegal River, at Médine just below the Félou waterfall (1855). By 1860, Faidherbe had built a series of forts between Médine and St. Louis, launching missions against the Trarza Moors in Waalo (north of the Sengal river), who had previously collected taxes on goods coming to Saint - Louis from the interior.

French Military forces had previously avoided conflicts with the most powerful states in the area, the Toucouleur empire along the Niger River, and the Cayor in the south. By sending emissaries to sign protectorates with weaker states (Bubakar Saada of Bondu, King Samba of Khasso) and by completing the "pacification" of Casamance and the Wolof peoples through what is now northern Senegal, Faidherbe quickly came into direct conflict with these states.

To accomplish even the first part of his design, he had very inadequate resources, especially in view of the opposition from El Hadj Umar Tall, the Muslim ruler of the countries of the middle Niger. By advancing the French outposts on the upper Senegal, and particularly by breaking Umar Tall's siege of Medina Fort, Faidherbe stemmed the Muslim advance. Striking an advantageous treaty with Umar in 1860, Faidherbe brought the French possessions into touch with the Niger. He also brought into subjection the country lying between the Senegal river and Gambia.

Faidherbe's large scale projects included the building of bridges and provisioning of fresh drinking water. But Saint - Louis' place as a door of French trade into an African interior began to wane with the expansion of direct colonial rule. Access to its port became increasingly awkward in the age of the steamship and the completion of the Dakar - Saint Louis railroad in 1885 meant that up-country trade effectively circumvented its port. Large French firms, many from the city of Bordeaux, took over the new commercial networks of the interior, marginalizing the Métis traders who had always been the middle men of upstream commerce.

Faidherbe also placed under direct French control large scale seasonal Groundnut cultivation near the fort systems, and then along the rail lines. This created the navétanes system of seasonal labor migration, first in Cayor, then spreading along the rail lines to Baol and Sine - Saloum, and eventually along the Thies - Kayes railway. This would be a pattern spread throughout French West Africa and French Equatorial Africa well into the 20th century.

When he resigned his post French rule had been firmly established over a very considerable and fertile area and the foundation laid upon which his successors built up the position occupied after 1904 by France in West Africa.

The first half-century of French colonialism in Senegal produced neither solid political control nor economic gains. However, it established the basic principles for the later French advance. Senegal became the principal French base, not Guinea. French expansion was aimed towards the interior (which also encouraged expansion south in Algeria), and Faidherbe's vision of empire was confirmed.

In 1863 he became general of brigade. From 1867 to the early part of 1870, he commanded the subdivision of Bona in Algeria, and was commanding the Constantine division at the commencement of the Franco - Prussian War.

After the defeat of Napoleon III and his French Imperial Army by the Prussian Army in the summer of 1870, colonial officers such as Faidherbe were recalled to France and increasingly promoted to higher ranks to command new units and replace generals killed or captured in battle. Faidherbe was promoted to general of division in November 1870, and on 3 December he was appointed commander - in - chief of the Army of the North by the Government of National Defence.

Faidherbe quickly proved himself to be the most able of the generals fighting Prussian forces in the French provinces, and won several small victories against the Prussian First Army at the towns of Ham, Hallue, Pont - Noyelles, and Bapaume. Despite his military skills, Faidherbe was never able to form an army strong enough to seriously worry the Prussians, as his army, composed of raw recruits, suffered immense supply difficulties and low morale in the freezing winter of 1870 - 71. The Army of the North performed remarkably well by being able to strike isolated German forces and then retreat behind the belt of fortresses protecting the Pas - de - Calais, but the army was ultimately destroyed at St Quentin when, ordered by Minister of War Leon Gambetta, Faidherbe rushed his army into an open battle with Prussian forces, which shattered Faidherbe's forces.

After the war, Faidherbe was elected 5 January 1879 to the National Assembly for the département of the Nord, He resigned his seat prior to the end of his term in 1888.

For his military services he was decorated with the grand cross, and made chancellor of the order of the Legion of Honor. In 1872 he went on a scientific mission to Upper Egypt, where he studied the monuments and inscriptions. An enthusiastic geographer, philologist and archaeologist, he wrote numerous works, among which may be mentioned Collection des inscriptions numidiques (1870), Epigraphie phenicienne (1873), Essai sur la langue poul (1875), and Le Znaga des tribes sénégalaises (1877), the last a study of the Berber language. He also wrote on the geography and history of Senegal and the Sahara, and La Campagne de l'armée du Nord (1872).

He was elected a senator in 1879, and, in spite of failing health, continued to the last a close student of his favorite subjects. He died on 29 September 1889, and received a public funeral. Statues and monuments to his memory were erected at Lille, Bapaume, Saint - Quentin and Saint - Louis, Senegal. Numerous streets are named after him and also a subway station in Paris (Faidherbe - Chaligny).