In his concern for the widows and orphans of those killed by the plague, he created several "Recolhimentos" (shelters) known as the "Recolhimento de Santa Marta" (shelter of Santa Marta) and the "Recolhimento dos Meninos" (shelter of the children) and provided wet nurses to take care of the babies.
Sebastjan je ustanovil štipendije (1568) za študente, ki so želeli študirati medicino ali farmacijo na Univerzi v Coimbri.