He built a wooden fort, covered with straw, and called it "Presépio de Belém", or the Crib of Bethlehem.

It was alleged that Caldeira be removed from that post "where he causes a thousand disturbances, unsettles the Indians, and puts someone else in their place to keep them as it suits him so they do not rebel".

The captains Paulo da Rocha and Thadeus dos Passos, friends of Alvaro Neto, pressured Francisco Caldeira to arrest his nephew.

Caldeira, however, set him free a few days later claiming that his nephew would be needed for a coming conflict with indigenous peoples.

He was jailed and deposed without resistance; Baltasar Rodrigues de Melo took his position as Governor General of the Captaincy of Grão-Pará.