This success caused a strong reaction of the traditionalist Patriarch of Alqosh, Eliya XII (XI) Denkha, who succeeded in having Joseph III imprisoned many times by the Turkish authorities.
[5]: 210 The patriarchate struggled with financial difficulties due to the tax burden imposed by the Turkish authorities and to the ransoms required to free Joseph from the prison.
Furthermore, according to the Ottoman law, the Chaldean community was administratively subject to the traditionalist Patriarchate of Alqosh, causing it to be in a weak position and exposed to vexations.
In 1734 Joseph left for Europe to try to raise funds to pay his debts, and during the next seven years he visited the Catholic courts of Poland, Austria and Rome asking for financial support.
In 1754 Joseph appointed as successor Mar Antun Galla, but the Holy See objected and did not allow him to resign: thus he remained the incumbent till his death on 23 January 1757.