In 2017, Baumgart signed with SC Paderborn. Having been saved narrowly the previous year, the club surprisingly finished second in the 2017-18 season and returned to the 2. Bundesliga. In 2019, in a remarkable turn of events, the newly promoted side managed another top-two finish, which returned Paderborn to the Bundesliga after years of turbulence. The 2019–20 season, however, saw the club struggle against Bundesliga competition. Paderborn finished the season in last place with 20 points, which led to their relegation back to the second tier in June 2020. Baumgart's contract at Paderborn was dated until 30 June 2021. In April 2021, it was announced that Baumgart will not extend his contract, and he left the club at the end of the season.
