Another wave of Jewish migration from Cranganore to Cochin happened soon afterward in the 15th century following a violent clash between them and the Arab traders over business matters. The large-scale damage inflicted on their homes and synagogues (Jewish place of worship) left even the wealthy Jews insecure in their old neighbourhood. They sought out the relative protection of Cochin. But changes in the political climate of Kerala affected the lives and fortunes of Cochin Jews seriously. The arrival of the Portuguese on the shores of Kerala was one of them. The already strained relations between the King of Cochin and the Zamorin, the ruler of Malabar, worsened with the former extending his arm of friendship to the foreigners in a bid to strengthen his political power in the region, and to contest the superiority of the Zamorin.
The Portuguese extended military support to the King of Cochin to vanquish the Zamorin but it was not long before they asserted their right over the land by building schools, founding churches, strengthening spice trade, and establishing power. The Cochin Jews were affected by the aggressive rule of the Portuguese that followed. As a result, when the Dutch landed in the 17th century as the Dutch East India Company, the Jews pledged alliance to the newest invaders in order to take revenge on the Portuguese. But following a military defeat, the Dutch withdrew to Ceylon (present-day Sri Lanka) and the Portuguese had their revenge on the Jews during which the Paradesi Synagogue suffered extensive damage. In the power struggle that took place shortly thereafter, the Dutch became victorious. This brought a period of peace and advancement in the community of Cochin Jews, especially among the Paradesi Jews (Jews who claimed to be of “pure” European or Middle-Eastern descent, as opposed to Malabari Jews of mixed race with both European and native blood). However, in course of time, after the British took over the reins of administration in the country, Paradesi Jews who were wealthier lost the special privileges accorded to them during the Dutch colonial rule. The competition with other merchants took more toll on their finances whereas the Malabari Jews prospered.
In the late 18th century during the Second Anglo-Mysore War, Tipu Sultan (the ruler of the erstwhile Kingdom of Mysore) invaded Kerala. Along with the rest of the populace, the Jews too suffered hefty losses during his raids. It is said that the Kochangadi Synagogue (the oldest synagogue in Cochin built-in 1344) was destroyed by the Mysore army.
At the time of the Indian Independence, there were close to a few thousands of Cochin Jews in the state.