Its discovery was later recorded by Father Gaspar Frutuoso in the seminal history of the Azores, Saudades da Terra, as he began: "This island of São Miguel where...we are, is mountainous and covered in ravines, and it was, when we discovered it, covered in trees...due to its humidity, with its water showers and ravines warm with sun..." It was sometime after the initial settlement of Povoação Velha (on the southeastern coast) that (between 1439 and 1444) a volcanic eruption occurred in the crater of Sete Cidades (then uninhabited).

In the early 15th century, Prince Henry the Navigator first authorized the settlement of the Azores, and many settlers from the historical provinces of Estremadura, Alto Alentejo, Algarve and Madeira travelled to São Miguel, under the Carta Régia (a decree of the regency).

(i.e., many had surnames such as Pereira, Pimentel, Dias, Menezes, Oliveira, Nunes, Castro, Pinheiro, Rosa, Furtado, Ferreira, Lima, Fonseca, Machado, Franco, Elias, Teixeira, Duarte, Souza, Pacheco, Almeida, Cardoso, Mendes, Gouveia, Estrela, Carneiro, Melo, Morreira, Cruz, Figueira Mesquita, Josué, Salvador, Teles, Meira, Silva, Amorim, Alvarez, Brandão, Miranda, Mota, Ribeiro, Aguiar, Soares, Coelho, Carvalho, Gomes, Mascarenhas, Henriques, Rodrigues, Costa, Pinto etc.

During the Portuguese succession crisis of 1580, the people from São Miguel won the naval Battle of Vila Franca against a French squadron that supported the claims of the pretender António, Prior of Crato.

With the Portuguese Restoration War (1640), the island regained its position as a commercial centre, establishing new contacts in Brazil, which was heavily colonized during this period.

In 1831, during the Liberal Wars, following the landing of troops loyal to Queen Maria II in Nordeste (sent by future Duke of Terceira), a resistance to the Absolutist regime on the Island was organized.

In 1832, this militia declared allegiance to the Charter (constitutional monarchy) and Queen Maria, forming a contingent that sailed to the continent where they were involved in the liberation of Porto.

Following the Liberal Wars, the period of Devourism allowed the economy to flourish, and the port of Ponta Delgada expanded, through the export of new crops such as tea, pineapple, and tobacco.

Following the Carnation Revolution, the island received the seat of the Presidency of the Autonomous Region of the Azores, located in Ponta Delgada, while its economic, social and political importance continued to grow within the archipelago.

São Miguel is bisected by many faults from the northwest to southeast in the direction of the Terceira Rift, a triple junction of the African, Eurasian, and North American tectonic plates.

This formation integrated lavas, basaltic pyroclasts, tuff cones and trachyte domes into two layers (referred to as the Ponta Delgada and Penhal da Paz sub-deposits) and compiled to about 5,000 years ago.

In addition, there are several communities that have developed within ancient craters (such as Sete Cidades, Furnas or Povoação), river-valleys (such as Ribeira Chã, Pilar da Bretanha) or coastal deltas (Mosteiros).

Two cities have developed, largely because the island was divided by mountainous volcanic cones in the interior: Ponta Delgada and Ribeira Grande.

Administratively, the island is governed by five municipalities, with Ponta Delgada and Ribeira Grande having more administrative functions associated with their larger populations: Lagoa, the youngest of the municipalities of São Miguel, has a population of about 14,126 inhabitants (2008 census), incorporating the south-central parishes east of Ponta Delgada; Nordeste, literally the north-eastern municipality, well known for an abundance of natural vegetation and the highest point on the island, Pico da Vara; Ponta Delgada, includes not only the industrial/commercial city of Ponta Delgada, but also many rural parishes, as well as the large crater of Sete Cidades; Povoação, home to the first colony on the island, Povoação is located in the south-east corner of the island, and includes active and dormant volcanic features, including Furnas and the crater of Povoação; Ribeira Grande, the second largest municipality, with approximately 30,852 inhabitants, received its charter in 1981, and incorporates an extensive area of the northern coast (including the parish of Rabo de Peixe, the largest parish by population); and Vila Franca do Campo, once the seat of the historical capital of São Miguel (until it was almost destroyed by earthquake and landslides in 1522), it is located along the southern coast between Lagoa and Povoação.

Government is administered at the local level by the civil parish (Portuguese: freguesias), which are responsible for the provision of services and implementation of municipal initiatives.

On the island of São Miguel there are 64 local area authorities, that include: Three bus routes operate in Ponta Delgada on weekdays from 07:00 to 19:00.