A constituent of the sui iuris Latin Church, the diocese was established in 1557 after the domination of the Portuguese-speaking missionaries.

[7][1] After its erection as a diocese, it was the second and preceded southern and eastern India, Burma, and Ceylon (now Sri Lanka).

The Syrian Bishop of those Christians promised obedience to the pope through the Franciscan missionaries and two Nestorian priests, who later accompanied Gama to Lisbon en route for Rome.

The pioneer priests of the diocese, Franciscans João d'Elvas and Pedro d'Amarante until 1507, preached the Gospel at Vypin, Pallippuram, and Kodungallur.

[citation needed] The Papal Bull of Pope Paul IV, which was used earlier in erecting the diocese was also utilised in raising the collegiate church of the Holy Cross, and the parish church of Cochin to a cathedral of the diocese with the first Bishop of Cochin, a Dominican Father Jorge Tremudo.

The city was reduced in size; the clergy were expelled; the monasteries and colleges, bishop's palace, etc, were razed to the ground.

The church of St. Francis of Assisi, belonging to the Franciscan monastery was spared by the conquerors and converted for their religious use.