He was one of the promoters of the annexation of Central America to the Mexican Empire of Agustín de Iturbide, which he favored over Guatemala.

The following year he aided Conservative José Justo Milla in his defeat of Honduran Chief of State Dionisio de Herrera.

From his position in the assembly, he promoted the separation of Honduras from the Federal Republic of Central America in October 1838.

That day, the constituent assembly declared El Salvador independent of the Central American Federation, and Lindo became president of the now-independent republic, serving until 1 February 1842.

Lindo signed an alliance with Salvadoran president Doroteo Vasconcelos to declare war on the government of Guatemala, headed by Rafael Carrera.

Allied troops invaded Guatemalan territory, but were defeated by Carrera in the Battle of La Arada on 2 February 1851.