The cathedral is considered one of the finest examples of Mannerism in the Portuguese empire and strongly resembles the Jesuit Church of Coimbra.

The interior of the cathedral has a large nave, elaborate baroque-style side altars, a sacristy, library, and ossuary.

Three Jesuit church buildings were erected on the site of the present-day cathedral, the final being destroyed during the Dutch occupation of Brazil.

[2][3] The Dutch, upon their entry into Salvador in 1624, stripped the interior of the Jesuit college of its silverwork and a relic reportedly used by St. Francis Xavier.

Salvador was reoccupied by the Portuguese in 1625, but the church and most buildings of the city were heavily damaged and remained under siege by the Dutch until 1654.

Housing for three religious communities, the father, the Escolásticas, and the Brotherhood; a smaller chapel; a refectory and kitchen; a novitiate; and a small school were completed soon after the opening of the church.

The novitiate was moved to the lower city in 1728 to the present-day Casa Pia and College of the Orphans of Saint Joachim.

Soares moved the entire community of Jesuits on January 7, 1760 into the domestic chapel of the college and sealed the doors and windows.

The members of the community, now prisoners, were taken by armed soldiers to Novitiate of Jiquitaia in the lower city; other troops guarded the route to ward off observers.

It façade faces west and church doors open to the wide Terreiro de Jesus, a public square.

The façade is made in light Lioz stone brought from Portugal, a feature also found in the Basilica of the Immaculate Conception in the lower city of Salvador.

[2] The chapels of the cathedral offer an interesting showcase of altarpiece art from the late 16th through the mid-18th centuries, all decorated with sculptures and paintings.

They were painted by Charles Belleville (1657-1730), a Jesuit who had lived in Macau for ten years prior to his arrival in Bahia.

The tomb of Mem de Sá's, the third governor-general of Bahia, is located beneath high altar.

[7] It was described in 1703 in the diary of an anonymous author as having "walls, floors, and a ceiling of jacaranda wood with fine paintings; extraordinary furniture, cabinets and gilded closets; with true perfection of joinery."

[4][2] The sacristy cabinet dates to the 17th century and has paintings of the life of Jesus on copper panels with an altar in the center.

The coffered ceiling of the sacristy has wooden panels painted with Mannerist motifs and portraits of noted members of the Jesuit order.