1920-1940 he lived permanently in Kaunas, 1940-1954 he worked in Vilnius, but in his free time he would return to Kaunas where his family lived.
In 1920, after the invasion of Vilnius by L. Želigovski, he found himself in Kaunas and was appointed a representative of the Lithuanian government to the military control commission of the League of Nations, which was to resolve the armed conflict between Lithuania and Poland. He worked there until 1922.From 1922 to 1924, he was the director of the Department of the League of Nations and the Polish Department in the Ministry of Foreign Affairs, and from 1924 to 1929, he was a freelance deputy to the heads of the various departments.
He was educated and spoke several foreign languages, and therefore took part in many international negotiations and conferences.
In 1929, together with others, he founded the Lithuanian Society for the Knowledge of the Culture of the Peoples of the Union of Soviet Socialist Republics (USSR); he was a member of its board, secretary, librarian, and chairman in 1938-1939.
1924-1932 - lecturer at the Department of History of the University of Lithuania, from 7 June 1929 - docent. At the end of 1931 he became head of the department, in 1932 - professor. He lectured on the history of Russia, Poland, France, Latvia and Prussia, but the most interesting were the lectures on the history of Lithuania, which were lithographed and published by students in three volumes.
For the Lithuanian Encyclopaedia, which was published in 1931, he wrote articles on princes, nobles, political figures and treaties, as well as on sources of history. He wrote studies on Michael the Lithuanian and "On the customs of Tatars, Lithuanians and Muscovites", but his greatest work is "Vytautas' Family" (1932).
In 1933, he was the head of the course for teachers of Lithuanian history. One of his most talented students was Adolfas Šapoka.
I. Jonynas started to create a scientific library in Kaunas.
1944-1946 he worked at both Vilnius and Kaunas universities, later only in Vilnius.
On the occasion of the 100th anniversary of the professor's birth and 30th anniversary of his death, a book was published in the series "Monuments of Lithuanian Science". Jonynas. In 1991, a memorial plaque was unveiled in Žaliakalnis, on the house at 3 Rūtų St. 3, with the following inscription: "The historian, professor Ignas Jonynas lived in this house in 1927-1954."
In 2008, the street planned in Maironiškiai was given the name of I. Jonynas.
