Nobleman Afonso de Albuquerque was returning from the conquest of Malacca, bringing with him a large treasure trove for the Portuguese king, when the ship was lost off the coast of Sumatra.

However, her return trip in 1503 met some complications—once loaded with spices, her large size and weight made her hard to manoeuver, particularly in the fast currents of the Mozambique Channel (notably, around Cape Correntes).

Nova attempted to take her out repeatedly, but the heavy-laden ship kept running into problems, forcing him to return to the island, repair and try again.

The ship and her frustrated captain were still stuck in Mozambique when they were found in February 1507—almost exactly one year after Flor do Mar left India—by the outgoing 8th India armada under the command of Tristão da Cunha.

In the aftermath, to Nova's surprise, Cunha ordered her to remain in the western Arabian Sea, integrated into the patrol squadron of Afonso de Albuquerque.

João da Nova died that same year in Cochin, and Almeida (ending his term as vice-roy) planned to bring Flor do Mar back to Portugal himself, taking special care to repair her into shape.

unsafe, Flor do Mar served to support the conquest of Malacca, then the largest commercial center of the East Indies.

Given her large capacity, Afonso de Albuquerque decided to use the ship to transport the vast treasure looted from the Sultan of Malacca's palace back to Portugal.

The lost treasure of the Flor de la Mar plays a significant role in the 2022 BBC Doctor Who episode Legend of the Sea Devils.