The independent Macedonian Orthodox Church was established under communism. The first initiative toward this end took place shortly before the end of the World War Two, when the Initiative Board for the Organization of the Macedonian Orthodox Church was formed in the village of Gorno Vranovci. In March 1945, the First Assembly of the Clergy and Laity in Skopje passed the resolution to restore the Archbishop of Ohrid as the (autocephalous) Macedonian Orthodox Church. This decision was submitted to the Holy Synod of the Serbian Orthodox Church, since before World War Two the Orthodox parishes of Macedonia were under the authority of the United Orthodox Church of Serbs, Croats and Slovenians, known as the Serbian Orthodox Church, seated in Belgrade. The Synod of the Serbian Orthodox Church did not accept this decision. As a result, the Initiative Board in Macedonia reformulated its petition and, instead of demanding the creation of an autocephalous church, asked for the recognition of the Macedonian Church as an autonomous entity. This request was also rejected by the Serbian Orthodox Church. In 1958, the Second Assembly of the Clergy and Laity in Macedonia was held in Ohrid. It accepted the proposal to restore the Archbishop of Ohrid as the head of the Macedonian Orthodox Church. The first appointed Macedonian archbishop was Dositej.
The Holy Synod of the Serbian Orthodox Church finally accepted the decisions of the Macedonian Assembly of the Clergy and Laity in 1959. As a sign of agreement, a liturgy was concelebrated together with the Serbian Patriarch German in the church of Saint Menas in Skopje on July 19, 1959. At the same time, Kliment was ordained as bishop of Prespa and Bitola. This meant that the Holy Synod of the Serbian Orthodox Church gave autonomy to the Macedonian Orthodox Church, which remained in canonical unity with the Serbian Church under their Patriarch. A few days later, in the church of St. Nicholas in Štip, Naum was ordained as bishop of the diocese of Zletovo and Strumica. The Holy Synod of the Macedonian Orthodox Church was established together with other administrative bodies in the Archdiocese and the dioceses in conformity with the statute of the Macedonian Orthodox Church.
In 1967, the Holy Synod in Ohrid proclaimed the Macedonian Orthodox Church as autocephalous, which was a result of conflicts with the Serbian Orthodox Church. No other Orthodox church has officially accepted the autocephalous status of the Macedonian Orthodox Church.