In 1510, the Portuguese defeated the ruling Bijapur sultan Yusuf Adil Shah with the help of a local ally, Thimmayya or Timoji, a privateer. They set up a permanent settlement in Velha Goa (Old Goa). This was the beginning of Portuguese colonial rule in Goa that would last for four and a half centuries, until its annexation by India in 1961. The Goa Inquisition, a formal tribunal, was established in 1560, and was finally abolished in 1812.

From the latter decades of the eighteenth century, the territory of Goa was composed of two segments: the central nucleus of the Velhas Conquistas (Old Conquests)—Bardes, Ilhas de Goa, and Salcette—which territories had been under Portuguese administration since the sixteenth century; and the Novas Conquistas (New Conquests)—Bicholim, Canacona, Pernem, Quepem, Sattari, and Sanguem—territories which had been successively added through the eighteenth century.[citation needed]

In 1787, Goa experienced its first revolt from its Catholic elite, with the Pinto Revolt led by a Goan noble family who revolted against the Portuguese due to racial discrimination in administration and clergy. They were betrayed by a member of the revolt. The Portuguese government executed some of the family members, while others, such as Abbe Faria, went on to join the French Revolution. This remains legend in Goa today.