His half brothers and sisters, Pedro Joaquín, Dionisio, Carmen, Mercedes and Fernando, grew under his guardianship.

In 1843, Fruto Chamorro was appointed Supreme Director of the Confederation junta, and he took up residence in San Miguel, El Salvador.

He then convened a Constituent Assembly on 20 January 1854, to promulgate a new Constitution during the absence of the majority of the western (Liberal Party) representatives, virtually expelled from the country by the government's move to Granada.

In March, Fruto Chamorro relinquished his title as Supreme Director and with acquiescence of the Assembly, named himself President of Nicaragua.

The Liberals saw this as a restoration to power of the provincial oligarchy, continuation of a feudal economic system, and the diminished possibility of an alliance of all Central American reactionary forces as well.

In preparation for the siege, President Chamorro placed himself at the headquarters of the Army and left executive authority with his deputy, José María Estrada.