He was the son of Miguel Álvaro Pinto da Fonseca, Alcaide-Mór de Ranhados, and his wife, Ana Pinto Teixeira. The coat of arms of the Pinto portrays five red crescents, to symbolising that the Pinto de Fonseca family won five battles with the Ottomans. Before his election as Grand Master on 18 January 1741, Pinto da Fonseca was a knight of the Langue of Portugal. He had an illegitimate son by one Rosenda Paulichi, daughter of Alberigo Paulichi and Patronilla Ramuzetta, named José António Pinto da Fonseca e Vilhena, who married his first cousin Maria Inácia Pinto da Fonseca de Sousa Teixeira e Vilhena, illegitimate daughter of Francisco Vaz Pinto by one Clara Cerqueira. He was elected as Grand Master in his 60th year, and he lived to be a nonagenarian, ruling the Order for 32 years. As Grand Master, Pinto da Fonseca kept an elaborate court, imitating the courts of the great European princes of his era. The court was a center of intrigue, the Grand Master being surrounded by a multitude of "ambitious pretenders". In 1749, one of his bodyguards, Giuseppe Cohen, refused to join a plot led by Pasha Mustafa to stage a Muslim slave revolt; this refusal led to the exposure and suppression of the revolt, which afterward was celebrated each 29 June, the anniversary. Pinto da Fonseca made substantial donations to the Conventual Church, and among the most notable mementoes are two large and heavy bells cast by the Master Founder of the Order of Saint John, Aloisio Bouchut, in 1747 and 1748; they still hang in the belfries of what is now the Co-Cathedral. These bells were made by melting two basilisks that were left by the Ottomans after the Great Siege of 1565. As Grand Master, Pinto da Fonseca completed construction of the Auberge de Castille ; his bust and arms adorn its façade. Today this building houses the Office of the Prime Minister. Pinto built nineteen storehouses at the Marina, which still bear his name, and built several other buildings and structures. In 1756, he has built the first printing press in Malta at the magistral palace of the Grand Master, known as la stamperia del Palazzo. Pinto gave his name to the then town of Qormi and accorded it the status of a city as "Città Pinto". The city of Qormi adopted the Pinto arms, with the tinctures reversed, for its own coat of arms and flag. Pinto gained a bad reputation for creating large debts for the treasury of the Order, leading to bankruptcy. In 1764, Pinto da Fonseca negotiated with King Frederick II of Prussia a reunification of the Protestant Bailiwick of Brandenburg with the Catholic Order of Saint John, but as Pope Clement XIII would not allow admission into a Roman Catholic organization of men viewed as heretics by the Church, the agreement came to naught. In 1765/6, Pinto was befriended by Italian adventurer and occultist Alessandro Cagliostro. A Master Mason of Freemasonry, don Pinto initiated to the 33rd degree don Raimondo di Sangro, prince of Sansevero, which later established the first Scottish Rite Masonic Lodge in Naples, Italy. Malta since 1734 was nominally a fief under the House of Bourbon-Two Sicilies, from 1759 under Ferdinand III. Bernardo Tanucci pressured Pinto to follow the Bourbon policy of suppression of the Jesuits, threatening a boycott of Malta if he refused. Pinto consulted with Pope Clement XIII, who reluctantly agreed to the expulsion of the Jesuits from Malta, insisting that it should be done "with due decency". Pinto signed the decree of expulsion on 22 April 1768. Twenty Jesuits were expelled, while three elderly Jesuits, two of them native Maltese, were allowed to remain. After the expulsion of the Jesuit Order, Pinto appropriated all the revenue accruing from its property on the island with the aim of establishing a Pubblica Università di Studi Generali. The decree constituting the University, now the University of Malta was signed by Pinto on 22 November 1769, having been authorised to do so by the Papal brief, Sedula Romani Pontificis, received on 20 October 1769. By 22 November of that year, the Grandmaster signed a bando establishing the University. Pinto died on 23 January 1773, aged 91. His body was laid in a neoclassic monument with his mosaic portrait. A statue of Pinto is found in Floriana.
