His presidency was marked by the end of the Federalist Revolution in southern Brazil and the War of Canudos, a peasant revolt in the northeast of the country that was crushed by the Brazilian Army.

[2][3] Morais wanted to move to São Paulo, where he could take preparatory courses for the Faculty of Law, but his stepfather was against his decision, despite the expenses being covered by the inheritance left by his father.

[4] Like many other leaders of the Brazilian Republic, in the faculty Morais joined the Bucha, a secret student society of a liberal, abolitionist, and republican nature founded by German professor Julius Frank and inspired by the Burschenschaft associations.

[2] Morais graduated with a Legal and Social Sciences degree in 1863 and moved to Piracicaba the following year, where he opened a law firm and began to work as an attorney.

After the proclamation of the Republic in 1889, his Party began to dominate national politics, and Morais was elected to the Constituent Congress as Senator for São Paulo.

Morais ran in the first Brazilian presidential election (conducted by the Constituent Congress after the promulgation of the Constitution and in accordance with its transitional provisions), but lost to incumbent head of the Provisional Government Deodoro da Fonseca.

The four-year government of Prudente de Morais was shaken both by partisan political issues and continued fighting in Rio Grande do Sul, the center of the Federalist Revolt (1893–1895).

Shortly after the rebel movement in Rio Grande do Sul, Prudente faced an even greater challenge: the War of Canudos in the interior of Bahia.

Forced to undergo surgery, Prudente de Morais retired from power between 10 November 1896 and 4 March 1897, turning over his responsibilities to vice president Vitorino.

Morais interrupted his convalescence and then appointed Minister of War general Carlos Machado de Bittencourt [pt] to lead a new expedition to defeat the rebels.

With the advice of his ministers of finance, Rodrigues Alves and Bernardino de Campos, Morais negotiated with British bankers to consolidate debt in a financial transaction known as the funding loan, based on the policy implemented by Joaquim Murtinho within four years.

In foreign policy, in 1896 Morais faced a diplomatic issue involving the British, who took possession of the islands of Trindade and Martim Vaz in 1895, and the revolt of the Military School.

Prudente de Morais re-established relations with Portugal and signed a Treaty of Friendship with Japan in November 1895 with the aim of encouraging the arrival of Japanese immigrants.