António was born in Lisbon, the illegitimate son of Prince Luis, Duke of Beja (1506–1555)[3] and Violante Gomes[4] (some sources argue that his parents were later married, perhaps at Évora).

He was asked the meaning of the cross of St. John that he wore on his doublet, and he replied that it was the sign of a small benefice which he held from the Pope, something he would lose if he were not back in Portugal by 1 January 1579.

[10] While António was a prisoner in Morocco, his uncle Henry, the cardinal archbishop of Évora and only surviving brother of King John III of Portugal (1521–1557), was proclaimed the new monarch.

His cousin, Catherine, Duchess of Braganza, was also a granddaughter of Manuel I, by her father the Infante Duarte, Duke of Guimarães, and was by this time the only legitimate Portuguese member of the royal family.

Cardinal Henry was torn between the two former claimants, dismissing António, albeit tending towards Philip II given the latter's assurances that Portugal would retain formal independence as well as autonomous administration of both its European territory and its empire.

The regency of the kingdom was then assumed by a governing junta composed of five members, with the Cortes increasingly leaning towards Philip II, given Catherine's limited support, particularly following her uncle's death.

The question of illegitimacy in 1580, however, was viewed very differently from 200 years earlier, underlined by the precedent of the Duke of Coimbra, only surviving son of King John II.

António and his supporters were decisively defeated in the Battle of Alcântara by the Spanish Habsburg armies led by Fernando Álvarez de Toledo, Duke of Alba on 25 August.

[12] He then attempted to rule Portugal from the island of Terceira, in the archipelago of the Azores, where he established an opposition government that lasted until 1583, and where he even minted coin — a typical act of sovereignty and royalty.

[12] Meanwhile, on the continent and in the Madeira Islands, power was exercised by Philip II, who was officially recognized as king the following year in the Portuguese Cortes of Tomar.

As the Habsburgs had not yet occupied the Azores, he sailed for them with a number of French adventurers under Philip Strozzi, a Florentine exile in the service of France, but was utterly defeated at sea by the Álvaro de Bazán, 1st Marquis of Santa Cruz at the Battle of Ponta Delgada, off the coast of the island of São Miguel between 25 and 26 July 1582.

He then returned to France and lived for a time in Rueil near Paris: fear of assassins, employed by Philip II, drove António from one refuge to another until he finally went to England.

In addition to papers which he published to defend his claims, António was the author of the Panegyrus Alphonsi Lusitanorum Regis (Coimbra 1550), and of a cento of the Psalms, Psalmi Confessionales (Paris 1592), which was translated into English under the title of The Royal Penitent by Francis Chamberleyn (London 1659), and into German as Heilige Betrachtungen (Marburg, 1677).