After a ceasefire was declared on July 31, 1941, the civil administration became limited to the provinces of El Oro and Loja until the Rio Protocol was signed on January 29, 1942, with Peruvian troops withdrawing on February 12.

Conflict broke out on July 5, when shots were fired between both parties alongside the Zarumilla River,[3][4][5] leading to the Peruvian Northern Army Detachment's land and air campaign in southern Ecuador and thus beginning the main stage of the Ecuadorian–Peruvian War.

[8] By the time the ceasefire had been accepted, the cities bombarded by Peru included Santa Rosa, Machala and Puerto Bolívar.

[11] The Peruvian administration immediately started efforts in order to exploit the newly acquired territories in southern Ecuador.

A civil administration was established in order to provide a sense of normalcy to the Ecuadorian citizens that lived under occupation, which relieved the military from certain efforts.

[12] Also prior to the evacuation, a general state of disorder had taken over due to a lack of administration, with both countries reporting looting by some Ecuadorian troops fleeing north.

According to Peruvian accounts, the Ecuadorians had attempted to cross the Chirá river into Peruvian territory in order to carry out an offensive against local troops commanded by Commander Carlos Herrera Lynch in nearby Pampa Larga, and were held back from this advance in the aforementioned battle.

Like with Macará, the town of Zapotillo was occupied and vacated days later, since their orders were to safeguard the areas of Pampa Larga and Remolino.

Novoa had been ordered to head the mission, which would travel on the Peruvian occupation's side of the Jubones River, with a detachment under his command.

The mission was ambushed by Ecuadorian troops, with only two sergeants from the 5th Cavalry Regiment surviving, and a Civil Guard member being taken prisoner.

[15] As a reprisal against the attack, the Peruvian Air Force bombarded the Ecuadorian outposts on the banks of the river and the Palao–Tenguel region, with preparations being made for the occupation of the area.

[6] As had happened one week prior, the Peruvian Air Force bombarded the area of El Placer, where the Ecuadorian troops were headquartered, in reprisal for the ambush.

The exiled Cantonal Council held its first plenary Session on January 18, six days after the withdrawal of Peruvian troops from Ecuador.