In 1925, he began teaching at the university and he then published his first work on the two Estonians dialects of Western Ingermanland.

[4] At age 28 (1928–1929), he was elected the Extraordinary Professor of Finnic Languages of the University of Tartu after the success of his 1925 thesis.

[4] As a result of the German invasion and subsequent conquest of Estonia from the Soviets, the fieldworkers for the University of Tartu were forced to join the German military list, which included Mägiste, but were still allowed to continue their fieldwork.

[4] In 1943, while Estonia was under German occupation, Mägiste made a visit to West Ingria.

Due to his involvement with the Germans and further Soviet advances into the Baltics, Mägiste fled Estonia for Germany in 1944 before then fleeing to Sweden.