[3] On April 10, Orbegoso recognized South Peru as an independent state through a decree, and a Supreme Court was installed in Cuzco on August 24.

[3][9] After a trade war, the Congress of Chile approved the declaration of war on December 26, 1836,[10] claiming that Santa Cruz's rule over Peru was illegitimate, and that his influence threatened the integrity of other South American nations, as seen by Orbegoso's support for an attempted invasion of Chile by Ramón Freire, specifically pointing out that it targeted then minister Diego Portales.

[11] Argentina followed suit after Juan Manuel de Rosas then declared war on the Confederation on May 19, 1837, after the escalation of a territorial conflict in its border,[12] accusing Santa Cruz of harboring supporters of the Unitarian Party.

[13] South Peru was invaded from October to November under the nominal leadership of Antonio Gutiérrez de la Fuente as Supreme Chief of Peru.,[14] with the occupants being surrounded and forced to sign the a treaty, leaving the country shortly after.

[10][15] The treaty was declared null and void by Chile,[16] and a second expedition headed by Manuel Bulnes was organized,[17] which left for Peru on July 19, 1838.

[10] Around the same time, North Peru seceded from the Confederation on July 30,[18] but was nevertheless attacked and defeated by the second expedition in the Battle of Portada de Guías of August 21.

From 1837 to its dissolution were a Provisional President and a Congress, both with limited powers and under the control of Marshal Andrés de Santa Cruz, who was styled the Supreme Protector.