In the Balkan Wars, Protogerov was one of the organizers of the Macedonian-Adrianopolitan Volunteer Corps and Assistant Commander of this military unit. During the First World War, he commanded the Third Infantry Brigade of the 11th Macedonian Infantry Division and then became commander of the Bulgarian troops in the Pomoravlje region of Serbia. There he suppressed the Toplica Uprising, commanding an army that committed a large number of war crimes, including cruel murders of thousands of women, children and the elderly. Later, as commandant of Sofia, Protogerov suppressed the Bulgarian soldier's uprising. After World War I, Protogerov was elected as one of the leaders of IMRO. In 1924, IMRO entered negotiations with the Comintern about collaboration between the communists and the Macedonian movement and the creation of a united Macedonian movement. Protogerov and Petar Chaulev probably signed the so-called "May Manifesto" about forming a Balkan Communist Federation and cooperation with the Soviet Union in Vienna. Later, Protogerov denied through the Bulgarian press that they had ever signed any agreements, claiming that the May Manifesto was a communist forgery. Shortly after, Todor Alexandrov was assassinated in unclear circumstances and IMRO came under the leadership of Ivan Mihailov, who became a powerful figure in Bulgarian politics. In 1925 Protogerov was injured in result of the organized by the communists St Nedelya Church assault. In IMRO itself, a major split arose between Mihailov's wing, supported by Andrey Lyapchev, and Protogerov's wing, supported by Aleksandar Tsankov. The faction led by Protogerov opted for continuing with the tactics of guerrilla warfare, while this led by Mihailov insisted on individual terrorist attacks. The result of this split and communists conspiracies was further strife within the organisation and several high-profile murders, including that of Protogetov himself.