The headquarters of the Flores Museum is in the Convent of São Boaventura and is responsible for managing the Baleia do Boqueirão Factory. The factory was built by Francisco Marcelino dos Reis to use sperm whale oil and produce guanos. The work took place between 1941 and 1944. It was owned by several owners and closed in 1981.
The Convent of Saint Boaventura has its origin in a donation deed by Father Inácio Coelho, brother of Friar Diogo das Chagas, dated 1641. The Franciscans remained there until the advent of liberalism. António Vicente Peixoto Pimentel bought the convent in 1873 to donate it to the Holy House of Mercy of Santa Cruz das Flores, to establish a hospital to serve the people of Flores and Corvo. The building retained these functions until the late sixties of the last century. At that time it was adapted to the school and in 1993, after extensive restoration work, reopened at the service of the Flores Museum.
It has a palatial facade in which horizontality predominates. It is characterized by a sharp angularity and intense planimetry of its compositional elements. The church is a relatively large and tall building, rectangular in shape, without transept and a single cylindrical nave of painted wood. The altarpieces are in golden cedarwood. On the ceiling predominates a vegetal and floral decoration.