The Flor do Mar and her captain João da Nova participated in Cunha's conquest of Socotra. 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. Nova and the ship participated in the Albuquerque-led conquest of the cities of Curiati (Kuryat), Muscat in July 1507, Khor Fakkan, (accepting also the submission of the cities of Kalhat and Sohar) and Ormuz in the same year. Two years later in India, she was commandeered to serve as the flagship of D. Francisco de Almeida in the 1509 battle of Diu. João da Nova died that same year in Cochin, and Almeida (ending his term as vice-roy) planned to bring the Flor do Mar back to Portugal himself, taking special care to repair it into shape. But his successor, Afonso de Albuquerque, forbade it and retained the ship in India, giving Almeida another ship to take home instead.[3]
Under Afonso de Albuquerque's orders, the Flor do Mar supported the conquest of Goa in 1510 as well as the conquest of Malacca in 1511.