He was succeeded as Governor by Henrique de Menezes, one of the captains who had accompanied him on the outward voyage, who then set about making appointments of his own.
Da Gama's eldest son, Dom Francisco, had remained at home to look after the family's interests at home, but the second and third sons, who had accompanied their father, immediately lost their positions and joined the returning fleet early in 1525, along with those da Gama had dismissed and deposed.
Both, however, returned. Dom Estevão, the second son, had a three-year term as captain of Malacca, was replaced by his younger brother, Paulo, then resumed the position when his brother died in a naval action off Malacca. He also served as the eleventh governor of India from 1540 to 1542.
Dom Cristóvão, the fourth son, served as captain of the Malacca fleet from 1538 to 1540 and was slated to succeed in Malacca, but was captured and executed on crusading duties in Somalia in 1542.
The last two sons, Dom Pedro da Silva da Gama and Dom Álvaro d'Ataide da Gama served as captain of Malacca from 1548 to 1552, and 1552 to 1554 respectively. Dom Alvarado was also captain of the Malacca fleet in the 1540s.
Their father's body was buried at St. Francis Church in Cochin, but the remains were returned to Portugal and re-interred in Vidigueira in 1539.