The situation was resolved when Fernando Coutinho, Count of Marialva and marshal of Portugal arrived in Cannanore on the next fleet from home. The squadron took Albuquerque back to Cochin and Coutinho had enough authority to force Almeida to hand over the reins.
Albuquerque took over as Governor and Captain-General rather than Viceroy in November 1509. Almeida left the following day but was killed, along with some fifty others in an ambush at the Cape of Good Hope on the return voyage.
In the meantime, Sequeira had tried to establish contact with the Sultan of Malacca in September, but negotiations failed, and he was forced to depart, leaving behind nineteen Portuguese prisoners and an excuse for Albuquerque to take action against the Sultanate.
Capturing Calicut was the primary objective for Marshal Coutinho's armada of fifteen ships and three thousand men, but an assault in January 1510 was unsuccessful. Coutinho, fascinated by the city's riches, was ambushed when he ignored instructions and ventured into the inner city. Albuquerque was wounded during the rescue, and the Portuguese were forced to retreat.
From there, Albuquerque turned his attention to Goa. An initial assault with twenty-three hips and 1200 men between 4 March and 20 May 1510 was successful, but declining support from the city's Hindu population, insubordination among the Portuguese ranks and the city's weakened fortifications made it difficult to hold.