[6] 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.

As Grand Master, Pinto da Fonseca completed construction of the Auberge de Castille[7] (still one of the most important buildings in the Maltese capital city, Valletta[8]); his bust and arms adorn its façade.

[11] 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.

[15] In 1764, Pinto da Fonseca negotiated with King Frederick II ("Frederick the Great") 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.

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".

[18][19][20] 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.