In the general election of October he was re-elected, local enthusiasm for him being increased by the fact that the government had driven him from the mayoralty. In the Chamber he occupied himself especially with education, fighting the clerical system established by the Loi Falloux, and working for the establishment of free, obligatory and secular primary instruction. In 1880 he became president of the departmental council in Drôme. His support of the second Jules Ferry ministry and his zeal for the colonial expansion of France gave him considerable weight in the moderate Republican party.
He had entered the Senate in 1885, and he became minister of public works in the Tirard ministry (December 1887 to March 1888). In 1892 President Sadi Carnot, who was his personal friend, asked him to form a cabinet. Loubet held the portfolio of the interior with the premiership, and had to deal with the anarchist crimes of that year and with the great strike of Carmaux, in which he acted as arbitrator, giving a decision regarded in many quarters as too favourable to the strikers. He was defeated in November on the question of the Panama scandals, but he retained the ministry of the interior in the next cabinet under Alexandre Ribot, though he resigned on its reconstruction in January.
He was marked out for fierce opposition and bitter insult, as the representative of that section of the Republican party which sought the revision of the Dreyfus affair. On the day of President Faure's funeral Paul Déroulède met the troops under General Roget on their return to barracks, and demanded that the general should march on the Elysée. Roget sensibly took his troops back to barracks. At the Auteuil steeplechase in June, the president was struck on the head with a cane by an anti-Dreyfusard. In that month President Loubet summoned Waldeck-Rousseau to form a cabinet, and at the same time entreated Republicans of all shades of opinion to rally to the defence of the state. By the efforts of Loubet and Waldeck-Rousseau the Dreyfus affair was settled, when Loubet, acting on the advice of General Galliffet, minister of war, remitted the ten years' imprisonment to which Dreyfus was condemned at Rennes.
Loubet's presidency saw an acute stage of the clerical question, which was attacked by Waldeck-Rousseau and in still more drastic fashion by the Combes ministry. The French ambassador was recalled from the Vatican in April, 1905, and in July the separation of church and state was voted in the Chamber of Deputies. Feeling had run high between France and Britain over the mutual criticisms passed on the conduct of the South African War and the Dreyfus affair respectively. These differences were composed, by the Anglo-French entente, and in 1904 a convention between the two countries secured the recognition of French claims in Morocco in exchange for non-interference with the British occupation of Egypt. President Loubet belonged to the peasant-proprietor class, and had none of the aristocratic proclivities of President Faure. He inaugurated the Paris Exhibition of 1900, received the Tsar Nicholas II of Russia in September 1901 and paid a visit to Russia in 1902. He also exchanged visits with King Edward VII, with the king of Portugal, the king of Italy and the king of Spain. During the king of Spain's visit in 1905, an attempt was made on his life, a bomb being thrown under his carriage as he was proceeding with his guest to the opera. When his presidency came to an end in January 1906, he became the first President of the Third Republic to have served a full term. He retired into private life and died nearly 24 years later. In 1904 he was appointed a Knight of the Norwegian lion by King Oscar II of Norway.