He was president of the Federal Office for the Protection of the Constitution (BfV) from August 2012 until his temporary retirement in November 2018. His behavior and statements during the riots in Chemnitz in 2018 sparked much controversy. He was a member of the Werteunion until January 2022; according to him, membership had been dormant since May 31, 2021. On January 28, 2023, he became federal chairman of the Werteunion. He stood as a direct candidate for the CDU in the Suhl - Schmalkalden-Meiningen - Hildburghausen - Sonneberg parliamentary constituency in the 2021 federal election and was defeated by his competitor Frank Ullrich (SPD). On February 13, 2023, the CDU executive committee unanimously decided to initiate expulsion proceedings and immediately revoke his membership rights. In July 2023, a CDU district party court rejected the expulsion in the first instance and reversed the revocation of membership rights. Maaßen's election as a member of the CDU was not a success.

Since leaving the office of President of the Office for the Protection of the Constitution, Maaßen has attracted attention with statements that sparked controversy. CDU party friends publicly called on Maaßen to leave the party several times and distanced themselves from his statements.