The establishment of the church was undertaken after the
Treaty of Riga left a large amount of territory previously under the control of the
Russian Empire, as part of the
Second Polish Republic. Eastern Orthodoxy was widespread in the Belarusian
Western Belarus regions and the Ukrainian
Volhynia. The loss of ecclesiastical link due to the persecution of the
Russian Orthodox Church in the
Soviet Union, left the regional clergy in a crisis moment, and in 1924, the
Ecumenical Patriarchate took over establishing several autonomous churches on territories of the new states that were formerly wholly or partially part of the Russian Empire (Finland, the Baltic States, and Poland).
interwar period, however, the Polish authorities imposed severe restrictions on the church and its clergy. The most famous example, the
Alexander Nevsky Cathedral in Warsaw was destroyed. In Volyhnia a total of 190 Orthodox Churches were destroyed and a further 150 converted to
 Several court hearings against the
Pochayiv Lavra also took place.
Second World War most of the ethnically Ukrainian and Belarusian territories were annexed by the
Soviet Union, holding up to 80% of the PAOC's parishes and congregation, which were united with the recently re-instated
Moscow Patriarchate. The remaining parishes that were now on the territory of the
Polish People's Republic were kept by the PAOC, including most of the mixed easternmost territories such as around Chełm and Białystok. In 1948, under pressure from the Russian Orthodox Church, the Ecumenical Patriarchate granted the PAOC
Although most of the congregation is historically centered in the Eastern borderland regions with considerable Belarusian and Ukrainian minorities, there are now many parishes across the country, as a result of
Operation Vistula and other diaspora movements. There are also some adherents in
Brazil, resulted from the 1989 canonical union between the hierarchy headed by Metropolitan Gabriel of
Lisbon, formerly under the
Church of the Genuine Orthodox Christians of Greece, and the Polish Orthodox Church.
 The European bishops, however, have left the jurisdiction on 2000, which eventually resulted on senior Bishop
Chrysostom being raised to archepiscopal dignity. There are now parishes in the states of
Rio de Janeiro,
Paraíba, plus a monastery in
In 2003, following the decision of the Holy Sobor of Bishops of the Polish Autocephalous Orthodox Church, the
New Martyrs of Chelm and Podlasie suffering persecution during the 1940s were canonized.