The chapels, the doors and the upper church contain numerous stained glass windows that were created in France.

Due to the American Civil War and the resulting impoverishment of the diocese, the cathedral was not replaced for several decades.

[6] In 2007, Bishop Robert J. Baker and Rector Monsignor Joseph Roth announced plans to renovate and complete the cathedral.

The spire has open grill work that reduces the wind load on the steeple by allowing the air to flow through.

It originally served as the Chapel of the Blessed Sacrament, Prior to 1968, the bishop sat in front of the altar.

It was purchased during the American Civil War by Bishop Patrick Lynch, who had served as secret emissary to the Vatican for the Confederate States of America.

[11] The altar in this chapel is adorned with an Italian marble statue of the Madonna and the baby Jesus, sculpted by the German artist Ferdinand Pettrich.

The statue depicts Mary without a head covering, holding the child Jesus as a toddler, which distinguishes from similar sculptures.

This chapel is the main lower church, primarily used for overflow crowds at mass and as a gathering space after the service.

The chapel contains one altar with a custom, hand-painted altarpiece depicting John the Baptist over the South Carolina landscape.

The three sets of cathedral doors are surmounted by rose stained-glass windows with coat of arms in their centers; Bishop Jacques Fabre-Jeune, CS Monsignor Gregory Wilson, V.G.

After the archdiocese bought the organ, its builder, Gene Bedient, reinstalled in St. John the Baptist Cathedral in 1995.