He played a role in spreading Christianity in Japan during the early 17th century as the bishop of the diocese which included Nagasaki.
On March 30, 1594, Cerqueira left for Asia, reaching the Portuguese colony of Goa on September 22, and arriving in Macao on August 7.
Conversions were numerous, and despite a growing hostility from the shogunate, the Church existed in relative freedom, ordaining Japanese priests, establishing Christian communities and welcoming new missionaries.
This dispute centered around the desire of the Franciscans to proselytize in Nagasaki, while the Jesuits sought exclusive access to the region for their missionary activities.
A papal bull was issued, granting permission for all religious orders, including the Franciscans, to engage in preaching and missionary work.