In the period under examination, the Hellenism of Thrace and Eastern Rumelia suffered systematic blows from both Bulgarians and the Young Turks after 1908.

In addition, Thrace was a pawn in the international diplomatic game.

In July and August 1906 the great persecution of the Greeks of Eastern Rumelia took place. Demonstrations of armed bands and violent anti-Greek manifestations rapidly developed into pillaging, arson and vandalism not only in Philippopolis, the centre of the riots, but also in Pyrgos, Stenimachos, Anchialos and elsewhere. From September 1906 the Greek population of the area fled as refugees to Greece and eastern Thrace, while those who remained underwent Bulgarization.
In May 1914 new persecutions completed the extermination of 1906. With a special Greco-Bulgarian convention within the Treaty of Neuilly (1919) the two countries decided upon a voluntary exchange of populations. On the basis of this convention, Hellenic presence in Eastern Rumelia finally came to an end.

From 1900 onwards, armed Bulgarian bands living in hide-outs in the Bulgarian-speaking areas of Bunar-Hisar and Saranta Ekklisies, attacked centres of Greek population. The Bulgarian komitadjis sought, through violence and intimidation, the Bulgarization of the Greek population. This continued until 1911.

In the meantime, Athens was organizing a plan to protect the Greeks of Thrace and to awaken their national consciousness. It sent officials, teachers and commercial and insurance agents there. Georgios Kondylis and Stylianos Gonatas engaged in resistance activity. At the beginning of 1908 the Pan-Hellenic Organization was founded, with its headquarters in Athens. Its goal was resistance not only in Thrace but throughout all areas of 'unreedemed' Greece. During the same period the Political Organization was established in Constantinople. Its founding members included the secretary general of the Greek embassy in Constantinople, Ion Dragoumis, Captain Athanassios Souliotis-Nikolaidis and the deputy Giorgos Bousios, who was in collaboration with the committees of the Pan-Hellenic Organization. Stylianos Gonatas was in charge of the Thracian branch of the organization and with arms dispatched there the groups of Bulgarian komitadjis were dealt with summarily.

The Slav threat inspired the Ottoman Empire to a policy of friendship towards the Greeks.

Thus, generally speaking, the position of the Greeks of Thrace was a good one in this period. With the revolution of the Young Turks, the Greeks of Thrace, as all the Greeks of the Empire, hoped for the amelioration of their position believing in the declarations of equality and brotherhood. They were soon disillusioned, however, since the measures of the Young Turks against the Greek communities affected many of their privileges.

The economy of Thrace (arable and cattle farming and trade) was hit by heavy taxation and the wars. During the First World War and under the pretext of the 'military security' of the Turkish cities, a large part of the population of eastern Thrace was deported towards the hinterland of Asia Minor hinterland (as was the case with the population of western Asia Minor and Pontos). Many were forced to convert to Islam, and they were distanced from the Patriarchate and had no access to Greek schools. A large part of the male population was exterminated in amele taburu or labour batallions. Many fled as refugees to Greece.

Thrace was occupied by the Greek troops during the Asia Minor Campaign. But she would share the fate of the rest of Hellenism in the East as a consequence of the Catastrophe. Western Thrace, however, was annexed to Greece.