It took some time before Mar Athanasius could establish himself as the Metropolitan of the Church. One of the factors which helped him to attain this position was an order from the Government of Travancore (1852) giving him recognition as the Metropolitan. As head of the Church, he worked hard for the education of the clergy and for raising the moral standards of the people. He was also able to remove various social disabilities of the people. For understandable reasons in the early years of his episcopate, he did not identify himself too closely with the movement for reform. But having established his position, there was no doubt as to where his sympathies lay. From the beginning, there was opposition against him from those who feared that he would be in favour of the reform programme. The opposition became gradually strong and succeeded in enlisting the support of the Patriarch on its side. The opponents of Mathews Mar Athanasius had sent complaints about him to the Patriarch, who without a judicial enquiry appointed Pulikottil Joseph Mar Dionysius to supercede Mathews Mar Athanasius as Metropolitan. As a result of this struggle for power, the Church tended to be divided into two sections, one favouring reform and the other opposed to it.

Thomas Mar Athanasius, son of Abraham Malpan was consecrated by Mathews Mar Athanasius as his successor in 1869. Mathews Mar Athanasius is generally considered one of the ablest Metropolitans of the Syrian Church.

At this difficult time, the support of leaders from the clergy and the laity who had been inspired by the spirit of the reform movement was a source of great strength to the position taken up by their bishops.