In February 1929 the Holy Synod was formed consisting of: On 29 June 1929, at the Second Clergy-Secular Congress held in Korça, the "Statute of the Autocephalous Orthodox Church of Albania" was voted.
The Ecumenical Patriarchate refused to accept these actions, but was willing to give itself self-government and in parallel the use of the Albanian language in worship, preaching and ecclesiastical education.
In order to normalize relations with the Ecumenical Patriarchate, the Clergy-Laity Congress convened in Korça, in May 1936, with the participation of representatives from all 4 dioceses (ecclesiastical provinces).
Congress apologized to the Patriarchate; talks took place in Athens (13 March 1937) and a commission composed of Albanians went to Constantinople to finally settle the matter.
The canonical archbishop Christopher, was held under house arrest and on 19 June 1958 was found dead (according to the official version suffered a heart attack).
At this time the attempt to trample on religion and its representatives began; as well as the pressure of internment, imprisonment, and murder of clergy and laity.
Father Jani Trebicka was appointed General Secretary of the Holy Synod of the Autocephalous Orthodox Church of Albania.
On 11 August 2000, Kozma Qirjo died, and was replaced as Bishop of Apollonia by Archbishop Anastasios, who also acts as Viceroy of the Metropolitan of Gjirokastra.
It unanimously reviewed and approved the amendment and improvement of some articles of the Statute of the Autocephalous Orthodox Church of Albania, which highlighted, among others, the creation of two new Metropolises, Apollonia and Fier, and Elbasan.
On 7 April 2016, the Holy Synod convened, which approved the amendments to the Statute of the Autocephalous Orthodox Church of Albania.
In accordance with the Statute, following the proposal of the Clergy-Laity Council, the Holy Synod undertook to fill the vacancies of the newly established Metropolises through regular voting.
The Holy Synod then raised the Diocese of Amantias to the rank of Metropolitan in the person of Bishop Nathanail (Lavrioti, Stergiu).
On the 9th of December 2024, Archimandrite Anastas (Enkelejd) Mamaj was elected by the Holy Synod as (titular) Bishop of Kruja.