In Tartu, Puusepp continued to research, innovate and publish. He was a founding Editor of Eesti Arst (Estonian Physician). A 726-page work, Die Tumoren des Gehirns, was published in 1929, and then translated for a Spanish edition in 1931. Puusepp founded the medical journal Folia Neuropathologica Estoniana. Published from 1923 to 1939, it incorporated work not only from other Tartu researchers but also from international authors including Marburg, Freeman, his mentor Bekhterev, Walter Dandy, Walker, Guillain, and Alajouaine. The first volume of Die Neuropathologie chirurgische, a monumental 1400-page work, was released in 1931. The work remained unfinished due to the advent of World War II and Puusepp's failing health. His final work, Peaaju, tema töö ja tervishoid was published in Tartu in 1941.