Between 1560 and 1621, the Portuguese Captain Major and Governor of Ceylon, Filipe de Oliveriya was responsible for the demolition of over 500 Hindu temples. In 1575, the Chilapam Muneswaram Kovil in Chillaw was destroyed. This was followed in 1588 by the demolition of the Vishnu Kovil in Devinuwera, and the Mathoddam Tirukethieswaram Kovil in Matota. The capture of Jaffna in 1619 changed the nature of Portuguese control over the Tamil kingdom. No longer did the Portuguese exert control through a subject but sovereign royal family. Control was now direct. As a consequence, the spread of Christianity accelerated, as did the destruction of temples. The Nallur Kandasamy Kovil was demolished under orders given by de Oliveriya on 2 February 1621, the day he assumed office as the senior Portuguese official in Jaffna. In 1622, the last great Ariya Chakravarti temple, the Thirukonamalai Tiru Konesar Kovil in Trincomalee was also torn down. In both Jaffna and Trincomalee, temple masonry was used to enhance the fortifications being built by the new colonial masters to withstand assault by modern weaponry. In Jaffna and in other towns, the destroyed temples were provided the building blocks for churches.

Perhaps the greatest crime was de Oliveriya's destruction of the Saraswati Mahal, which held the Ola leaf and copper-plate inscriptions containing the history of the oldest written language in the world. This ancient museum and library, the repository of all the lore and history of the Tamil people, was destroyed without a trace.

The main Portuguese objective in Lanka was the exploitation of trade. As a consequence, once coastal areas were controlled (and therefore denied to a rival trade power), the Portuguese were content to limit their incursions into the interior. No effort was made to develop any infrastructure or trade in the Jaffna area. Early evangelism was encouraged however, and many Tamils who had experienced faith conversions through the proselytising efforts of Christian missionaries in the century since the Portuguese arrival, were joined by those converted by the sword, or through commercial expediency.

On 21 June 1658, the Dutch captured Jaffna, bringing to an end the thirty-seven and a half years of Portuguese occupation.