During the decline and dissolution of the Ottoman Empire, Muslims living in territories previously under Ottoman control often found themselves persecuted after borders were re-drawn. These peoples included Turks, Kurds, Albanians, Bosnian Muslims, Circassians, Serb Muslims, Greek Muslims, Muslim Roma, and Pomaks. They were subject to genocide, expropriation, massacres, religious persecution, mass rape, and ethnic cleansing.McCarthy, Justin Death and Exile: The Ethnic Cleansing of Ottoman Muslims, 1821–1922, Darwin Press Incorporated, 1996, , Chapter one, The land to be lost, p. 1Adam Jones. (2010).Genocide: A Comprehensive Introduction page 65 & 152. "Incorporating a global-comparative perspective on the genocide of the last half-millenium has enabled important advances in the understanding of events central to the genocide studies field – such as the process of Ottoman imperial dissolution, reciprocal genocidal killing (during the "Unweaving" in the Balkans)...The human toll of this "Great Unweaving," from Greece's independence war in the early nineteenth century to the final Balkan wars of 1912–1913, was enormous. Hundreds of thousands of Ottoman Muslims were massacred in the secessionist drive.."

The 19th century saw the rise of nationalism in the Balkans coincide with the decline of Ottoman power, which resulted in the establishment of an independent Greece, Serbia, Bulgaria and Romania. At the same time, the Russian Empire expanded into previously Ottoman-ruled or Ottoman-allied regions of the Caucasus and the Black Sea region. These conflicts such as the Circassian genocide created large numbers of Muslim refugees. Persecutions of Muslims resumed during World War I by the invading Russian troops in the east and during the Turkish War of Independence in the west, east, and south of Anatolia by Greek troops and Armenian fedayis. After the Greco-Turkish War, a population exchange between Greece and Turkey took place, and most Muslims of Greece left. During these times many Muslim refugees, called Muhacir, settled in Turkey.

Background

The Turkish presence and the Islamisation of native peoples in the Balkans

Ottoman military expeditions shifted from Anatolia to Europe and the Balkans for the first time with the occupation of the Gallipoli peninsula in the 1350s.Norman Itzkowitz, Ottoman Empire and Islamic Tradition. University of Chicago Press, 2008, , p. 12 After the region was conquered by the Muslim Ottoman Empire, the Turkish presence grew. Some of the settlers were Yörüks, nomads who quickly became sedentary, and others were from urban classes. They settled in almost all of the towns, but the majority of them settled in the Eastern Balkans. The main areas of settlement were Ludogorie, Dobruja, the Thracian plain, the mountains and plains of northern Greece and Eastern Macedonia around the Vardar river.

Between the 15th and 17th centuries, large numbers of native Balkan peoples were forcibly converted to Islam. Places of mass conversions were in Bosnia, Albania, North Macedonia, Kosovo, Crete, and the Rhodope Mountains.Conversion to Islam in the Balkans: Kisve Bahas ̧petitions and Ottoman Social Life, 1670–1730, Anton Minkov, BRILL, 2004, . Some of the native population converted to Islam and became Turkish over time, mainly in Anatolia.The Geography of the Middle East, Stephen Hemsley Longrigg, James P. Jankowski, Transaction Publishers, 2009, , p. 113.

Motives for the persecution

Hall points out that atrocities were committed by all sides during the Balkan conflicts. Deliberate terror was designed to instigate population movements out of particular territories. The aim of targeting the civilian population was to carve ethnically homogeneous countries.Hall, Richard C. (2002), The Balkan Wars, 1912–1913: prelude to the First World War, Routledge, pp. 136–137

Great Turkish War

Even before the Great Turkish War (1683–1699) Austrians and Venetians supported Christian irregulars and rebellious highlanders of Herzegovina, Montenegro and Albania to raid Muslim Slavs.

The end of the Great Turkish War marked the first time the Ottoman Empire lost large areas of territory in Europe to Christians. Most of Hungary, Croatia, Dalmatia, Slavonia, Montenegro, Podolia and the Morea were lost, and the Muslim minorities were killed, enslaved, or expelled to Muslim-ruled lands such as Bosnia. The Ottomans regained the Morea quickly, and Muslims soon became part of the population or were never thoroughly displaced in the first place.

Most of the Christians who lived in the Ottoman Empire were Orthodox and so Russia was particularly interested in them. In 1711 Peter the Great invited Balkan Christians to revolt against Ottoman Muslim rule.

Habsburg Empire

In 1697, Prince Eugene of Savoy's troops took advantage of a weakened Ottoman military presence in Europe and penetrated into Ottoman Bosnia, where they reached the capital city of Sarajevo. On 23 October, the Habsburg troops set fire to the city, which quickly spread out of control and scorched most of the city. Most mosques were burnt to the ground, and the majority of the imams and muezzins burned to death in the flames as well. Only a few mosques and a church reportedly survived the inferno. The city's Catholic population were evacuated alongside the Habsburg forces, who retreated from Bosnia on 25 October. They resettled in Slavonia, then a part of the imperial realm. The city took nearly two centuries to recover, still having less than half the pre-1697 population into the early 19th century.Velikonja, Mitja (2003). Religious Separation and Political Intolerance in Bosnia-Herzegovina. Texas A&M University Press. p. 121. .

After the Siege of Pécs, local Muslims were forced to convert to Catholicism between 1686 and 1713, or left the region. The city of Hatvan became a haven for Turkish merchants and became a majority-Muslim settlement, but after it fell to the Hungarian troops in 1686, all Turkish settlers were forcibly expelled and their holdings in the city became property of foreign mercenaries that fought in the Liberation of Buda.

About one quarter of all people living in Slavonia in the 16th century were Muslims who mostly lived in towns, with Osijek and Požega being the largest Muslim settlements. Professor Mitja Velikonja explains that Muslims and non-Slavs who lived in Hungary, Croatia (Lika and Kordun) and Dalmatia, had fled to Bosnia-Herzegovina, following the loss of the occupied territories in these regions after the Habsburg-Ottoman war of 1683–1699. Velikonja states that it was considered the first example of cleansing of the Muslim population in the area that "enjoyed the benediction of the Catholic Church". Around 130,000 Muslims from Croatia and Slavonia were driven to Ottoman Bosnia and Herzegovina.

Basically, all Muslims who lived in Croatia, Slavonia and Dalmatia left or were exiled, killed or enslaved by the Habsburg and Venetian conquests.

Thousands of Serb refugees crossed the Danube and populated the territories of Habsburg Monarchy left by Muslims. Leopold I granted ethno-religious autonomy to them without giving any privileges to the remaining Muslim population who therefore fled to Bosnia, Herzegovina and Serbia spreading anti-Christian sentiment among other Muslims there. The relations between non-Muslim and Muslim population of Ottoman held Balkans became progressively worse.

In the early 18th century, the remaining Muslims of Slavonia moved to Bosnian Posavina. The Ottoman authorities encouraged hopes of expelled Muslims for a quick return to their homes and settled them in the border regions.

The Muslims were two thirds of the population of Lika. Like the Muslims who lived in the rest of Croatia, they were forced to convert to Catholicism or be expelled. Almost all Ottoman buildings were destroyed in Croatia, after the Ottomans left.

Northern Bosnia In 1716, Austria occupied northern Bosnia and northern Serbia until 1739, when those lands were ceded back to the Ottoman Empire at the Treaty of Belgrade. During this era, the Austrian Empire outlined its position to the Bosnian Muslim population about living within its administration. Two options were offered by Charles VI: conversion to Christianity, retaining property and remaining on Austrian territory or a departure of the remaining Muslim to other lands.al-Arnaut, Muhamed Mufaku (1994). "Islam and Muslims in Bosnia 1878–1918: Two Hijras and Two Fatwās". Journal of Islamic Studies. 5. (2): 245–246.

"This being the case, the Muslim Bosnians could no longer imagine any existence for Muslims outside the devlet unless they lived outside the pale of the din, it cannot be denied that the attitude of neighbouring countries had influenced this state of mind. For after two centuries of stability and supremacy dār ar-Islām was no longer immune from attack. Muslims now faced a new, unexpected, inconceivable situation. The triumph of their Christian enemies meant that, in order to survive, the Muslims had to choose either to Christianize and remain inside the Christian state or to emigrate southwards in order to remain Muslims within the Muslim state. Thus we notice that Austria in particular, when changing from the defensive to the offensive, was concentrating on Bosnia, but without its Muslims. in the war of 1737–9 we find Emperor Charles VI, in the edict addressed to the Muslim Bosnians dated June 1737, outlining two options for them: 'whoever of them wishes to adopt Christianity, may be free to stay and retain his property, while those who do not may emigrate to wherever they want' They fared no better in the 1788–91 war, although Emperor Joseph I issued a proclamation in which he promised to respect Muslim rights and institutions. However, despite these pledges, the Muslims quickly disappeared from the areas ceded by the Ottoman Empire."

Montenegro At the beginning of the 18th century (1709 or 1711), Orthodox Serbs massacred their Muslim neighbors in Montenegro.

National movements

Serbian Revolution