The "New Cathedral" was originally the church of the Jesuit's university college in Coimbra, established in the city in 1543.

In 1759, the Jesuit Order was banned from Portugal by the Marquis of Pombal, Prime Minister of King José I.

The interior, covered with barrel vaulting, has one nave with several lateral chapels and a transept with a dome and cupola.

Both transept arms and the main chapel of the apse are decorated with huge, magnificent gilt wood altarpieces built between the 17th and 18th centuries which are fine examples of the so-called "national" Portuguese altarpiece style.

The 17th-century choir stalls of the main chapel were brought from the Old Cathedral, as was the intricate stone baptismal font, carved by Pero and Felipe Henriques in late Gothic-Manueline style in the beginning of the 16th century.