Within the framework of a state organization based on Western models, an attempt was made to reorganize the Church. The responsibility for the settlement of the church matter was assigned to Mauer, a professor and member of the regency, based on the suggestions of the archimandrite Theoklitos Pharmakidis. The royal decree issued on 23rd July-4th August 1833 declared the independence of the Church of Greece from the Ecumenical Patriarchate and its foundation charter was published. According to the charter, the Autocephalus Church of the Greek Kingdom was administered by the Holy Synod, a five-member organ in which clergymen approved by the king participated. Later decrees issued at the end of 1833 and in the first months of 1834 called for the abolition of men's monasteries with fewer than six monks and that of all but three convents. Finally, it provided that monastery possessions would devolve to the state.

The fact that the Church of Greece was declared Autocephalus without asking the permission of the Patriarchate provoked a rift with the Phanar. This divided Greek society which on the whole remained profoundly religious and still considered the Patriarchate as head of the Orthodox people. This atmosphere was exploited by the rivals of Pharmakidis, K. Oikonomou and his supporters, who doubted the legality of the separation from the Patriarchate. However, the dispute on the ecclesiastical question was exploited by the traditional social elites that were now out of power and felt deprived of their regional economical and socio-political supports; they undermined the work of the regency. Finally, after a 20-year dispute, the opinion of Oikonomou prevailed. The government and the Holy Synod submitted a petition to the Patriarchate for the acknowledgement of the Autocephalus property and the whole matter was settled with the publication of the Synodic Volume by the Patriarchate in August 1850.