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 Vijayanagar. Goa then started exporting spices to Arab nations, and got Arabian horses for the Vijayanagar army.
The mighty Vijayanagar Empire, with its capital at Hampi controlled most of southern India and Goa remained a part of their kingdom for almost 100 years. The Bahmanis were back again in 1470 under Mahmud Gawan when they regained control and made Goa an important part of their Deccan Kingdom.
In 1492, the Bahmani Kingdom split into five kingdoms, namely Bidar, Berar, Ahmednagar, Golconda and Bijapur. Goa came under the control of Sultan Yusuf Adil Shah Khan who ruled from the capital city of Bijapur.
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 former Secretariat building in Panaji is a Adil Shah palace, later taken over by the Portuguese Viceroys as their official residence.