The two Balkan Wars precipitated Bulgaria's first national catastrophe. After the signing of the Treaty of Bucharest in July 1913 Bulgaria lost its exarchate in European Turkey. The dioceses of the exarchate in Ohrid, Bitolya, Veles, Debur and Skopje passed to the jurisdiction of the Serbian Orthodox Church and the Salonika diocese was taken over by the Greek Church. The metropolitans of the five Macedonian dioceses were driven out by the Serbs and Archimandrite Eulogius, who was at the head of the diocese of Salonika, died by drowning at sea in July 1913. Only the metropolitan See of Maronia in western Thrace (whose titular resided in Gumurjina) remained under the jurisdiction of the Bulgarian Exarchate. The Bulgarian Church also lost its dioceses in southern Dobroudja; they passed under the jurisdiction of the Romanian Orthodox Church. In the parts of Macedonia under Serbian and Greek sovereignty, and in Romanian southern Dobroudja, the Bulgarian schools were closed and the Bulgarian teachers and priests expelled. Thereafter, the Bulgarian population was subjected to brutal assimilation.
After the Second Balkan War very few Orthodox Christians were left under Exarch Joseph's pastoral care (only in Constantinople, Adrianople and Lozengrad). For that reason, as primate of the Bulgarian Church, he decided to move the seat of the exarchate to Sofia. He left behind an Exarchal Deputation, which was governed until its closure in 1945 by Bulgarian hierarchs (the first to be appointed was the Metropolitan of Veles, Meletius). The deputation had the duty to look after the spiritual and physical welfare of the Bulgarian Christians in the Ottoman Empire and, later on, the Republic of Turkey. The Exarchal Deputation was planned as a future operational headquarters which, given favourable circumstances, was to restore the organization of the Bulgarian Church in Macedonia and the Adrianople region of Thrace.
Exarch Joseph spent a little over a year and a half in Sofia. His health was failing, but, as always, he was working tirelessly to strengthen the positions of the Church. After his death on 20 June 1915, thirty years passed before a new exarch and primate of the Bulgarian Church was elected. At the time of the exarch's death the international political situation was extremely complicated. The First World War had been raging for nearly a year, but Bulgaria was prudently keeping its neutrality. On 6 September 1915, however, a treaty with Germany was signed and the country threw in its lot with the Central Powers. At the end of September 1915 a general mobilization was ordered and on 14 October Bulgaria declared war on its western neighbours. After the country's entry into the war the Bulgarian Exarchate began to restore its external dioceses, lost a few years earlier. When at the end of November 1915 Bulgaria took back Vardar Macedonia from Serbia, the metropolitans of the Exarchate who had been expelled in 1912 returned there. Some of them remained in their dioceses until the end of their days. Thus, for example, the Metropolitan of Debur, Cosmas, died on 11 January 1916 in Kicevo and was buried in the neighbouring Monastery of the Immaculate Holy Mother of God. The Metropolitan of Strumica, Gerasimus, died on 1 December 1918 in Strumica, where he was buried.
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