The multi-purpose Franciscan
Convent of São Boaventura, utilized by the citizens as church, school and hospital
Antique Whaling Station and current Museum of Flores
The first attempts to settle Flores occurred in the area of Caveira where Willem van der Haegen and his supporters disembarked looking for the mythical Ilhas Cassitérides. After these colonists abandoned their settlement new pioneers in 1508 and 1510 attempted to succeed in the area of the present Santa Cruz.
This settlement was helped by the installation of the Franciscan Convent (São Boaventura), now a museum. Its construction began in 1642, two years after Portugal's Restoration of Independence, under the initiative of local Florense Father Inácio Coelho. The convent was renowned for its Baroque alter-pieces and its ornamented roof (constructed from local cedros-do-mato, typical of the region).
The Franciscans had a profound effect on the local population, installing the annual celebrations for the Culto do Divino Espírito Santo (Cult of the Holy Spirit), and becoming responsible for the education of the local community. Offering many courses, including Latin, it was their system that became the basis for the reforms in the post-Pomboline national educational system. But, after lasting briefly, those educators abandoned the island and the Franciscans returned to their place in São Boaventura. During the early transition between Franciscan and public systems, Father José António Camões, was important in his functions (between 1797 and 1807) exercising his role as the only grammar teacher on the island. He returned to this place in 1815, where he continued until 1827 in this capacity. Santa Cruz remained the only educational centre in the Western Group of Azorean islands, until the middle of the 19th century; it consolidated its position, forcing the local population to send their children to live in the regional capital in order to obtain an education. The convent, whose chief benefactor was Father Maurício António de Freitas, promoter of the religious foundation Externato da Imaculada Conceição, was also the primary establishment to provide post-secondary education after the fall of the religious orders. The nucleus of post-secondary education began in October 1959, in the home of the poet Roberto de Mesquita, until it was moved, much later, to the Convent of São Boaventura where it was transformed into a public institution.
The convent also became the home of the local hospital (now medical centre) for the island, founded in 1878, on the initiative of António Vicente Peixoto Pimentel (1827–1881). The hospital occupied the Convent, after the Pombolino expulsion of the religious orders (in 1834), which was at the time owned by Francisco da Cruz Silva e Reis. It was purchased in 1877 by the Santa Casa da Misericórdia de Santa Cruz das Flores as a formal hospital and children's shelter. After a campaign, spearheaded by Peixoto Pimentel, part of the convent was demolished and an extension remodeled to serve the hospital, which was re-inaugurated in 1881, the same year that its founder died. Until the 1940s the convent operated in this capacity, where it was closed until 1945 due to a lack of modern conditions. Part of the convent was demolished, and a new building built after the establishment of the French Communications Base. Apart from local doctors, French military doctors brought new equipment, forms of treatment and conditions that allowed the hospital to boast its eminence in the Azores, even realizing complex surgeries not available on the other islands.
The construction of the Matriz Church of Nossa Senhora da Conceição (English: Our Lady of Conception) began in the close years of the 18th century, after one attempt was impeded by a strong rock deposit near the Praça do Município (now the Praça Marquês do Pombal). Construction ended in 1859, after many years of difficult financial constraints and unexpected difficulties in its construction.
During the second half of the 19th century, the whaling industry was an important part of the island's economy. After a few years of traditional whale-hunting the industrialization of the activity was formalized with construction of factory, and whale oil and products were concentrated in the area of Boqueirão. The Fábrica da Baleia do Boqueirão (Whale Factory of Boqueirão), now a part of the Flores Museum, occupies an advantageous place in the area around the port of Boqueirão, with a ramp adapted to drag Sperm whales from the ocean. Its architect of this business was the Lisbon entrepreneur Francisco Marcelino dos Reis and directed by his partner José Jacinto Mendonça Flores, who was the local investor of Reis & Flores, provisioner to whaling fleets. Construction began in October 1941, and the machinery installed by March 1943. It is likely that the factory began operations in the summer of 1944, probably in the month of July. It continued to operate until 1976. After a couple of tentative attempts to restart operations, it was finally closed in 1981. At its peak (1963) the factory processed 103 whales. The final animal was processed on November 24, 1981 after José Jacinto Mendonça Furtado harpooned the 21st whale of the season.
Of the many stories of ships being sunk in the waters of Flores, owing to its rocky coastal shores, there is the strange story of the whaler Modena, from the port of Boston which floundered in the waters of Bermuda on April 22. Captain William H. Long and eleven men, after abandoning their ship, survived an adventure of 2,000 nautical miles (3,700 km) along the Gulf Stream to the mouth of Ribeira da Cruz, in Fajã do Conde. In this area, the sailors carved on the rocks: "Capt. W. H. Lang and 11 men landed May 5, 1873 from Bark Modena of Boston Mass. Foundered April 22".