[1][2] After two years of training at the prestigious Hospital Real de Todos os Santos,[3] he received surgical license in March 1546 by the Portuguese king.

Upon reaching Japan, he resolved to travel to Yamaguchi to meet the Jesuit father Cosme de Torres, who was in charge of the mission after Francis Xavier's departure, and from there the two kept in close contact.

His personal wealth and his continued involvement in the Sino-Japanese silk trade kept the Jesuits financially afloat and provided the funds for various charitable efforts in Japan.

For example, in the year of his accession he founded an orphanage in Funai (today Ōita) in the east of the island of Kyushu, because many children had lost their parents due to the fierce hegemonic struggles of the Sengoku period.

Initially, Almeida was in charge of the surgical department, and internal medicine was in the hands of converted Japanese doctors, who were so successful in applying Chinese-Japanese therapies that some of them were singled out by name.

Even after he began his work as a priest, he continued to invest in trade, raised funds for hospitals, and generously donated his personal fortune to the Japanese Church, which was suffering from chronic financial difficulties.

In 1565 he spent his time in the Kansai area, leaving descriptions of a Japanese tea ceremony he witnessed in Sakai and of the magnificent temples of Nara.