This period of cultural and economic development was cut short by political upheavals in the region, beginning in 1903 with the Macedonian rebellion against the Turkish rulers of the Ottoman Empire. Ethnic violence among Greeks, Serbs, and Bulgarians over the future of Macedonia exposed Monastir to political violence and economic disruption throughout the first decade of the twentieth century. As a result, thousands of Jewish Monastirlis (as the locals referred to themselves) emigrated to North and South America, Jerusalem, and the Sephardic metropolis of Salonika. After the end of the Second Balkan War in 1913, formerly Ottoman Macedonia was carved up among Serbia, Bulgaria, and Greece. Monastir, then renamed Bitola, was in the territory incorporated by Serbia. However, the Jewish community continued to call the city by the name it bore during centuries of Ottoman rule: Monastir.

At the turn of the twentieth century, Monastir's Jewish population reached nearly 11,000, but by 1914 years of emigration had reduced the community to just over 6,000. During World War I, Monastir suffered two invasions and two years of bombardment. More than 5,000 Monastir Jews fled their homes and lived as refugees in the surrounding area. When the war was over, Monastir's Jews numbered just over 3,000. Bitola became part of the new state of Yugoslavia, and in the 1920s and 1930s Zionism emerged as the dominant force among the local Jewish youth. During those years, 500 of these young men and women emigrated to Palestine.