Despite the king's efforts to maintain the peace, there were occasional outbursts of violence against the New Christians culminating in the Lisbon massacre in 1506.

The faithful were praying for an end to the drought and plague that were sweeping the country when several worshipers claimed they saw a strange light emanating from a crucifix in the Chapel of Jesus.

Word of the apparent miracle spread and soon the church was packed with a great crowd that included German and French sailors from trading ships in the harbor.

"They burnt them in the streets of the city for three days on end, till the bodies were consumed and became ashes", according to the eyewitness account of the New Christian Isaac Ibn Farad.

By Monday evening the violence seemed to be ending but Dominican friars from the Monastery of São Domingos organized a procession and urged the crowd to kill the "heretics" and "extinguish the wicked race".

The rampage continued until Thursday, when a religious procession calling for peace marched through the city and restored order.

[4] The king and the court had earlier left Lisbon for Abrantes to escape the plague, and were absent when the massacre began.

When King Manuel I was informed of events in Lisbon, he ordered the governor to hurry to the city and "hang all the evil doers responsible for the massacre".

Following the massacre, hundreds of New Christians ignored the royal decree forbidding emigration and fled Portugal while some who remained still felt deep allegiance to the Portuguese monarch.

Several contemporary accounts have survived including one by noted historian, Gaspar Correia, which was discovered at an auction house in the 1970s.