Immediately after retiring, Maaßen was named manager of his last club Drochtersen/Assel.[2] Drochtersen/Assel finidhed first and won promotion to the Regionalliga Nord during the 2014–15 Oberliga Niedersachsen season[3] and finished fourth during the 2015–16 season.[4] In the 2016–17 DFB-Pokal, Drochtersen/Assel were knocked out by Borussia Mönchengladbach.[5] They finished the league season in ninth place.[6] They finished 12th in the 2017–18 season.[7] On 7 March 2018, after nearly four years in charge, his club confirmed that he would leave the post at the end of the season,[8] and he was confirmed as manager of Rödinghausen for the 2018–19 campaign seven days later.[9]
On 12 June 2020, Maaßen was appointed manager of Borussia Dortmund's reserve team, replacing Mike Tullberg.[10] He renewed his contract until 2024 on 21 May of the following year,[11] and achieved promotion to the 3. Liga with the side on 7 June 2021 after a 2–1 win over Wuppertaler SV.[12] In the summer of 2022, he left Dortmund and joined FC Augsburg.[13] He was sacked in October 2023.[14]
On 8 June 2024, he was announced as FC St. Gallen's new head coach.[15]