The 14th century saw a series of Muslim invasions on Goa, from the north. In 1312 Govepuri was almost completely destroyed, and after 15 years of fighting, the Muslims returned under Mohammed Tughluk and Chandrapur was beaten down to ruins.
The Muslim kingdom of Bahmani conquered Goa in 1347. The temples in Goa were the target of the fanatic zeal of the invaders who murdered priests and looted the temple wealth. Devotees moved their deities to safer areas under Hindu control.
Many Hindus fled southward. The persecution continued till 1378, when Goa was retaken by the neighbouring Hindu kingdom of Vijaynagar. Goa then started exporting spices to Arab nations, and got Arabian horses for the Vijayanagar army.
During this period, a lot of bloodshed followed when the Bahmanis persecuted the Hindus on a mass scale. Hindu temples were razed and Govepuri was brought down to its last brick. After the destruction of Govepuri, the Bahmanis organised a new capital at Ela, created on the northern banks of the river Mandovi to facilitate trade through the sea routes as the Zuari had begun to silt up.
Yussuf Adil Shah of Bijapur built many impressive buildings and a wonderful palace. The Portuguese later used this palace which is now the Secretariat in Panaji, and the old story of affluence started again, and Gove became an important trading destination again. Gove also became a port from where Muslim pilgrims left for Mecca.