Schirmer was appointed Professor at the Hochschule für Musik und Theater in Hamburg in 2000, teaching musical analysis and musical dramaturgy. From 2006 to 2017, he was chief conductor of the Münchner Rundfunkorchester (Munich Radio Orchestra).[2]
From 2009 to 2022, Schirmer was General Music Director (Generalmusikdirektor, GMD) of the Oper Leipzig.[3] On 23 March 2011, Schirmer was elected Intendant of the Oper Leipzig, with an initial five-year term beginning in August 2011, in addition to his title as GMD.[4] He conducted the first Bayreuth staging of Wagner's early opera Die Feen in 2013.[5] In June 2017, Oper Leipzig announced the extension of Schirmer's contract as Intendant through the 2021-2022 season.[6] Schirmer stood down from both Oper Leipzig posts at the close of the 2021-2022 season.
His recording of Karl Amadeus Hartmann's Des Simplicius Simplicissimus Jugend[10] was awarded the ECHO Klassik [de] in 2010 in the category opera of the 20th/21st century. The work, commissioned by the Bayerischer Rundfunk, was performed in its reconstructed first version, with soloists Camilla Nylund and Christian Gerhaher. Other recordings include the violin concerto by Max Reger with soloist Ulf Wallin.