On May 18, 1838, the Federal Congress, meeting in San Salvador, authorized the States to organize themselves regardless of national laws, while the Fundamental Charter of the Republic was reformed, and as such, the Head of Honduras, Justo Herrera, who had been in command since 1837, called a Constituent Assembly, who declared, on October 12, 1838, the sovereignty and independence of the country.

The Assembly of Guatemala, meeting in January 1839, declared General Carlos Salazar Head of State, and Mariano Rivera Paz returned to the Government Council.

Morazán returned to San Salvador, and although welcomed with respect, he was defeated and he considered it preferable to choose the path of ostracism, marching with a group of his supporters to settle in David, which was then part of the Republic of Colombia.

On February 1, 1841, El Salvador also declared itself separated from the federal pact, which was already a fact since the Armistice of Saint Vincent with Honduras, on June 5, 1839, had established in its article 8.9 that "The Contracting States, they mutually guarantee their independence, sovereignty and freedom."

The dissolution of the Federation offered a unique opportunity for the ambitions of foreign powers to expand their domains at the expense of the dissolved nationality reduced to five divided and weak States.