The church is noted for its music program led by the Canon for Music, Martin Green.
There are three choirs: the regular adult choir that sings at the 10:30 Sunday Eucharist, and the Cathedral Choristers (boys and men) and the St Cecilia's Choir (girls and men) which alternate singing at weekly Evensong.
Many concerts are held at the cathedral, including chamber music and choral works, and are open to the public.
The cathedral is the home of the Pacific Academy of Ecclesiastical Music (PACEM) and maintains an extensive music library.

The cathedral's Aeolian-Skinner organ is a historical instrument that encompasses part of the first organ in the city of San Diego, built in 1887 and moved with the church to its present location in the 1950s.
It was expanded several times with additional ranks and keyboards.
In 2011, the Cathedral raised funds for organ restoration, and the instrument was dismantled and sent to Missouri for a complete restoration.
A temporary, digital organ was installed in its place.
The restored Aeolian-Skinner organ was back in place by December 2012.

The organ is used for weekly concerts (Tuesday at noon) in addition to its role in worship services.
The Civic Organist of San Diego since 2001, Carol Williams, is also Organist in Residence at St. Paul's.
The church is noted for its music program led by the Canon for Music, Martin Green. There are three choirs: the regular adult choir that sings at the 10:30 Sunday Eucharist, and the Cathedral Choristers (boys and men) and the St Cecilia's Choir (girls and men) which alternate singing at weekly Evensong. Many concerts are held at the cathedral, including chamber music and choral works, and are open to the public. The cathedral is the home of the Pacific Academy of Ecclesiastical Music (PACEM) and maintains an extensive music library.
The cathedral's Aeolian-Skinner organ is a historical instrument that encompasses part of the first organ in the city of San Diego, built in 1887 and moved with the church to its present location in the 1950s. It was expanded several times with additional ranks and keyboards. In 2011, the Cathedral raised funds for organ restoration, and the instrument was dismantled and sent to Missouri for a complete restoration. A temporary, digital organ was installed in its place. The restored Aeolian-Skinner organ was back in place by December 2012.
The organ is used for weekly concerts (Tuesday at noon) in addition to its role in worship services. The Civic Organist of San Diego since 2001, Carol Williams, is also Organist in Residence at St. Paul's.
St. Paul's Cathedral (San Diego)