After selling his rights to the Captaincy of São Miguel to Rui Gonçalves da Câmara, he continued as Donatary-Captain of Santa Maria.
In 1474, due to his wife's illness, Albergaria moved to the island of Madeira in order to "find remedies and medics", as well as a milder climate for her to convalesce in.
As Azorean chronicler Gaspar Frutuoso would later relate, due to São Miguel's perceived unproductivity and the many costs Soares de Albergaria incurred during his move to Funchal and treatments for his wife, Albergaria decided to sell the Captaincy of São Miguel to Rui Gonçalves for his hospitality in return for 2,000 cruzados and 60,000 kilograms (130,000 lb) of sugar.
[2] During his captaincy, Albergaria promoted settlement of Santa Maria—attracting settlers from both Portugal (mainly Algarve) and continental Europe—and founded the principal village of Vila do Porto.
Before this, his maternal uncle Gonçalo Velho Cabral had been "Commander of Santa Maria and Captain of the Azores" within a structural framework that was not properly defined.