Nicolau Coelho's caravel was back in Portugal on 23 June 1501, followed by Cabral on 21 July 1501. Of the thirteen ships that had sailed from Lisbon sixteen months earlier, six had been lost, and two returned empty.
The cargoes aboard the five fully loaded vessels in the fleet covered the cost of outfitting the original fleet, the value of the ships lost along the way and left a profit that exceeded the total outlay.
Cabral's return came three months after the departure of the Third India Armada, four ships under João da Nova departed, and news of the developments during Cabral's voyage meant the Fourth Armada, labelled the "Revenge Fleet", was going to be a larger and more complex operation. Cabral was initially placed in charge of preparations but was eventually relieved of the command.
He may have been dismissed, or may have requested to be relieved of the position. Whatever happened, the intrigue and factional infighting irritated Manuel to the point where mentioning the matter in the king's presence resulted in banishment from the court. The command went to Vasco da Gama, one of his supporters invoked the royal displeasure, and Cabral left the court permanently.
While he was out of favour with Manuel I, Cabral was able to marry well. His wife, Dona Isabel de Castro, was a wealthy descendant of Fernando I and one of Afonso de Albuquerque's nieces. While the marriage produced at least four children, details of Cabral's life after he withdrew to Santarém in 1509 are few and far between.
Sometime around 1518, he was promoted from fidalgo to knight in the King's Council with a monthly allowance of 2,437 reais in addition to the 30,000 a year he had been receiving since 1497. Cabral died around 1520 and was buried in a chapel of Santarém's Convento da Graça.