The majority of these Christians, as can be surmised, were Armenian. Furthermore, during the conflict with the Ottomans, Shah Abbas I was letting the Catholic sovereigns of Europe believe that, if he obtained their support, he would order all his Christian subjects to submit to the Catholic Church. However, the conflict between the Iranians and the Portuguese and the economic power of the Armenians, who belonged by a great majority to the Apostolic Church, made it unlikely that the Shah would make his Armenian subjects Catholic. The Carmelites tell us that the Armenians had stirred Shah Abbas I against the Augustin Fathers, telling him that the Augustins wished to make the Armenians Portuguese subjects. The peace with the Ottoman Empire made the Shah even less obliging towards the Catholic missionaries, and for a period he even refused to grant them an audience, as the conversion of the Armenians was an issue he did not wish to discuss.
The Catholic missionaries, however, persevered in their evangelical activities. They established schools to which they invited the Armenians to send their sons. The Archbishop of New Julfa did not wait long to threaten with excommunication all those who had their children tutored by Catholic missionaries. He even had Shah Abbas II expel Father Ambroise from Iran, as he was deemed to be an assertive Catholic militant. The Armenian ecclesiastics had even succeeded in obtaining an edict prohibiting the Augustin missionaries from officiating for Nestorian Christians. In 1654 they simply forced the Jesuits, Carmelites and Capucins to leave New Julfa. Many Armenians in Nakhchevan had been converted to Catholicism by a Dominican from Bologna, but Chardin says that the persecution by the Armenian patriarch had brought them back to the Apostolic faith. The Dominicans sent letters to the Safavid court from the Pope and the Catholic monarchs of France, Poland and Italy, asking the Shah to protect the Catholics in Iran.
After the death of Shah Abbas II, the struggle between the Armenians and the Catholic missionaries intensified even further. Agha Piri, who was the kalantar of New Julfa and probably the wealthiest Armenian of Iran, was staunchly opposed to the activities of the European missionaries. His conversion to Islam in 1673 increased even further his influence at the court, which he certainly used to frustrate the Catholics. During this period, the Armenians persuaded Shah Sulayman (1666-1694) to ban marriages between Armenians and Catholics. Knowing the delicate situation of the Armenians, the French missionaries and merchants lured the Armenian katholikos to appeal to the Pope and acknowledge his authority, but the Carmelites and the Augustins, seeing that they could not play any part in this political reconciliation, advised the Pope to ignore his appeal.