The establishment of the convent dates to 1542, when Brás Pires do Canto obtained a papal bull from Pope Paul III to authorize the first construction of a convent for the Sisters of Angra.
Destined for the contemplative orderof Poor Clares it was there that Brás Pires do Canto helped collect his two daughters who had followed the order and one whom eventually became the first abbess.

The growth in the number of novices during the 16th and 17th centuries resulted in the expansion of the primitive installations, which today represents the location of the church.
Remnants of this church, oriented towards the east, can still be seen in the vestiges integrated into the walls of the southern cloister.
After its expansion, the new church was consecrated at the end of the 17th century, although its interior decorations were not completed until the following century.
 In 1793, a new organ was commissioned and installed by António Xavier Machado e Cerveira.
The Church of Gonçalo de Amarante was inaugurated in 1776, sheltering the ancient Irmandade de Nossa Senhora da Boa Morte e Assunção (Sisterhood of Our Lady of Good Death and Assumption), an venerable order.

During the Liberal Wars, the arrival of Liberal forces caused great fury, illustrated by the Marquess of Fronteira, who affirmed: "...here everyone had a courtship...", implying that many sisters were tempted or fell victim to the soldiers.
This included, specifically, Teotónio de Ornelas Bruges Paim da Câmara and, supposedly, Pedro IV of Portugal himself, all these facts were not verified.

Following the extinction of the religious orders, after 10 May 1832, the Convent was the unique one to survive, receiving many of the Sisters from many of the surrounding islands.

At the end of the 19th century, the cloister was damaged by an earthquake, resulting in the necessary substitution of Tuscan columns and arches in the eastern part with pilasters.

As a result of the 1 January 1980 Azores earthquake, much of the convent and grounds were damaged or scarred.

It was classified as a Property of Public Interest (Portuguese: Imóvel de Interesse Público under decree 516/71, on 22 November 1971, a classification that was included in group of buildings making part of the Historical Centre of Angra do Heroísmo, under resolution 41/80, 11 June 1980.

A project to remodel the southern wing of the cloister was studied in 2005 by the Gabinete da Zona Classificada, but much of the budget was lost in this study, and not the actual work to restore the building.
In July 2006, the third phase of the restoration of the convent and cloister was begun, under the direction of architect Miguel Cunha, who created rooms for the treatment and care of seniors and formal residences for members of the convent.
The establishment of the convent dates to 1542, when Brás Pires do Canto obtained a papal bull from Pope Paul III to authorize the first construction of a convent for the Sisters of Angra. Destined for the contemplative orderof Poor Clares it was there that Brás Pires do Canto helped collect his two daughters who had followed the order and one whom eventually became the first abbess.
The growth in the number of novices during the 16th and 17th centuries resulted in the expansion of the primitive installations, which today represents the location of the church. Remnants of this church, oriented towards the east, can still be seen in the vestiges integrated into the walls of the southern cloister. After its expansion, the new church was consecrated at the end of the 17th century, although its interior decorations were not completed until the following century.  In 1793, a new organ was commissioned and installed by António Xavier Machado e Cerveira. The Church of Gonçalo de Amarante was inaugurated in 1776, sheltering the ancient Irmandade de Nossa Senhora da Boa Morte e Assunção (Sisterhood of Our Lady of Good Death and Assumption), an venerable order.
During the Liberal Wars, the arrival of Liberal forces caused great fury, illustrated by the Marquess of Fronteira, who affirmed: "...here everyone had a courtship...", implying that many sisters were tempted or fell victim to the soldiers. This included, specifically, Teotónio de Ornelas Bruges Paim da Câmara and, supposedly, Pedro IV of Portugal himself, all these facts were not verified.
Following the extinction of the religious orders, after 10 May 1832, the Convent was the unique one to survive, receiving many of the Sisters from many of the surrounding islands.
At the end of the 19th century, the cloister was damaged by an earthquake, resulting in the necessary substitution of Tuscan columns and arches in the eastern part with pilasters.
As a result of the 1 January 1980 Azores earthquake, much of the convent and grounds were damaged or scarred.
It was classified as a Property of Public Interest (Portuguese: Imóvel de Interesse Público under decree 516/71, on 22 November 1971, a classification that was included in group of buildings making part of the Historical Centre of Angra do Heroísmo, under resolution 41/80, 11 June 1980.
A project to remodel the southern wing of the cloister was studied in 2005 by the Gabinete da Zona Classificada, but much of the budget was lost in this study, and not the actual work to restore the building. In July 2006, the third phase of the restoration of the convent and cloister was begun, under the direction of architect Miguel Cunha, who created rooms for the treatment and care of seniors and formal residences for members of the convent.
Convent of São Gonçalo (Angra do Heroísmo)