By the time Kunjali, the Mappila leader, took over as the Zamorin’s captain and started capturing Portuguese ships and massacring their crew’s war broke out between Calicut and Cochin, the Portuguese assisting the latter and the Egyptian fleet of Sulaiman Pasha coming to the help of the former.
But the Egyptian fleet went back without giving any assistance to Calicut and the Portuguese gained the upper hand and defeated the naval forces under Kunjali. The Zamorin thought it wise to come to terms with the Portuguese and treaty was signed by which both agreed to abandon their proteges, and allies.
After ten years of peace, the Portuguese started subduing the feudatory chiefs of the Zamorin and attacked Vadakkumkur Raja, killing him and burning his palace. The Raja’s forces after a savage sally drove the Portuguese army. The action against Vadakkumkur infuriated the Zamorin who was the Raja’s relative, and to avenge the death of his scion, he took the field against the Portuguese. In the sea battle off the coast of Cannnore Kunjali was defeated by Luiz de Mello.
In 1569 the Zamorin established diplomatic relations with Adil Shah of Bijapur and Nizam Shah of Ahmednagar and their forces attacked the Portuguese simultaneously at Goa, Chaul and Chaliyam. The Portuguese succeeded in saving the first two but the last one fell to the Zamorin in 1571 who allowed them safe passage. They returned to Cochin in a state of depression.
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Hostilities did not terminate with the fall of Chaliyam fort. Naval warfare still continued. Portuguese successfully blockaded the sea to prevent rice trade between Tulunad and Calicut. The Zamorin again sought the assistance of the Adilshahis. Moreover the relations were strained between the Portuguese and the Cochin ruler over the issue of port dues. Therefore the Portuguese were forced to open negotiations with Calicut.
They succeeded in concluding a peace with the Zamorin in 1584 where by the right to establish a factory at Ponnani was conceded to them. As it was against the commercial interests of Muslims, Kunjali, the Calicut admiral opposed it and continued his hostile activities against the Portuguese ships.
He and his relatives and followers directed their operations from the fort at Pudupattanam on Zamorin’s territory and became so powerful and recalcitrant that the Zamorin was forced to seek the assistance of the Portuguese to disarm them. Kunjali defied his master, by adopting the royal titles of the “King of the Malabar Moors” and “Lord of the Indian Seas”. He even insulted the Zamorin’s messenger. In a joint action by the Zamorin and the Portuguese he was captured and put to death by the Portuguese in Goa.