According to the inscription over the main portico, the church dates from 1846,[1] the year António de Freitas (an ex-seminarian born in Fajãzinha, returned from Macau, where he had made his fortune in the traffic of opium and child slavery.[1] In his gratitude to God for saving his fortune ("as a sign of his recognition for the safety of all his possessions"), he decided to finance the construction of a new church, to the invocation of the Holy Trinity, in Mosteiro.[1]
The church was erected in an isolated urban area inserted into a level area and courtyard. In front of the church is the Império do Espírito Santo, that dates from 1879.[1][2]
The first burial in the new churchyard occurred on 8 October 1847.[1]
On 23 October 1850, by royal decree, Queen D. Maria II elevated Mosteiro administratively, forming (along with locality of Caldeira) the new parish of Mosteiro, that substituted the former Mosteiros[3] that dominated until then.[1] It was later supported by the elevation of the religious parish to the status of ecclesiastical parish on 18 November in the same year, by friar D. Estêvão de Jesus Maria, then bishop of Angra.[1]
From 1893 to 1896, the parish priest was Francisco Nunes da Rosa, whose Pastorais do Mosteiro (1904) is one of the first works of Azorean literature.[4]
From 1896 to 1915, the old chapel in the parochial church was expanded, under the initiative of Father Caetano Bernardo de Sousa, then the parish priest.[1] The collateral retables were designed and sculpted by Father Guilherme, priest for Mosteiro and Fazenda das Lajes.[1]
Between 18 November 1895 and 18 January 1898, the parish was integrated into the municipality of Santa Cruz das Flores, when the municipality of Lajes was extinguished.[1]