Later in life, while away governing São Jorge da Mina, he was slandered by his enemies at court with accusations of theft and corruption. He was recalled to the capital and briefly imprisoned until he was exonerated by the Crown being proved innocent. But the damage was done as he had lost his governorship, his wealth, and influence. Although he was acquitted his protector, King João II of Portugal had died and been replaced by a king who didn't acknowledge the value of Duarte Pacheco. Duarte Pacheco had served the previous king as a squire, and had served King Manuel merely as a high ranking servant. His distance from Lisbon and his success meant he had many enemies abroad, and few friends in the capital to defend him. He died alone and penniless.