From the 16th to the 19th centuries, Portugal shipped slaves into South America from western Africa. Brazil was the most common destination for African captives, with 42% of all enslaved peoples shipped across the Atlantic.

Most commonly sold into Brazil were Akan, Igbo, Yoruba, Dahomean, Muslim Guineans, Hausa, and Bantu (among them Kongos, Kimbundas, and Kasanjes) from Angola, Congo and Mozambique.

These Africans brought their cultural traditions and religions with them to the New World. There is contention as to whether the game arrived with enslaved Africans or whether Africans refined a preexisting Brazilian game. One catalyst for capoeira was the homogenization of African people under the oppression of slavery. Capoeira emerged as a way to resist oppression, secretly practice art, transmit culture, and lift spirits. Some historians believe that the indigenous peoples of Brazil also played an important role in the development of Capoeira.

Most Brazilian scholars have argued that Capoeira emerged as a way to conceal the fact that slaves were practicing to fight (against their owners), concealing it with a seemingly happy dance routine. This explains why today's Capoeira appears to be a mix of both fighting techniques and flowing artful dance.

Batuque and Maculele are other fight-dances also developed by African-descended populations that are closely connected to Capoeira.

After slavery was abolished in 1888, the freed people often moved to the cities of Brazil. With employment scarce, many joined or formed criminal gangs. They continued to practice Capoeira, which in time became associated with anti-government and criminal activities. As a result, Capoeira was outlawed in Brazil in 1890, and the punishment for practicing it was extreme (practitioners would have the tendons on the backs of their feet cut), and the police were vicious in their attempt to stamp out the art. Capoeira continued to be practiced, but it moved further underground. Rodas were often held in areas with plenty of escape routes, and a special rhythm called cavalaria was added to the music to warn players that the police were coming. Capoeira practitioners (capoeiristas) also adopted apelidos or nicknames to make it more difficult for police to discover their true identities. To this day, when a person is baptized into Capoeira at the batizado ceremony, they may be given an apelido. (Legal persecution of the art faded eventually.)

Mestre Bimba made a major contribution to the preservation of the art by opening the first academy for instruction in Capoeira. This was a significant development because it eventually led to the legalization of the art in Brazil, and allowed Capoeira to gain popularity at a time when the art could possibly have died out. A notable example of the influence of Mestre Bimba's system of formal instruction took place in 1937, when he was invited to perform with his students at an event at which Getulio Vargas (the president of Brazil at that time) was present. Vargas was so impressed with the discipline and devotion of Mestre Bimba's students he declared Capoeira one of the national sports of Brazil.

In 1942, Mestre Pastinha opened the first formal academy for instruction in the traditional form of the art, known as Capoeira Angola. Mestre Pastinha's efforts prevented Capoeira Angola from being lost as newer, modernized forms of the art gained popularity.

This era was a milestone of a dramatic change in the mode of instruction of the art of Capoeira. Previously, Capoeira was passed on in secret, usually from a relative such as one's father or uncle, or in a small group setting where several young people in a particular community would receive guidance from elder practitioners from that community. During this era, the academy system became the predominant form of participation in the art. Presently, there are capoeira academies on almost every continent of the world.

Another significant change that occurred due to the proliferation of Capoeira 'schools' is the participation of middle and upper class members of the population.