Виленский край
At the end of World War I, he returned to Lithuania and joined the People's Commissariat of Education of the Lithuanian Soviet Socialist Republic. After the failure of the Soviet government, he lived in Vilnius, worked as a school principal, and opposed Polish ambitions in the city. For a few months in mid-1920, he was the chief Lithuanian commissioner in the Vilnius Region. After the 1920 Żeligowski's Mutiny, during which Polish forces captured Vilnius, Jonynas moved to Kaunas and joined the control commission of the League of Nations to negotiate the dispute over the Vilnius Region. After the diplomatic efforts failed in 1922, Jonynas continued to be employed by the Ministry of Foreign Affairs of Lithuania until 1929. From 1924 until his death, he lectured at the University of Lithuania and Vilnius University, attaining professorship in 1932.