The present structure of the cathedral was built in 1998-2002 in cruciform, of which the candle-like design is appropriate to the cathedral's patron. Inside the main church is marble statue of the Immaculate Conception designed by Philippine National Artist for Sculpture Napoleon Abueva. Along the aisles are the stained-glass symbolic images of all dioceses in Mindanao from 1910 to 1984. The day chapel at the ground floor is used for weekday masses. Fronting the day chapel is the baptistery with the relic of Our Lady of the Pillar, the patroness of the city. Behind the day chapel is the columbarium with a replica of Michelangelo's "Pietà" and the stained-glass images of the 12 apostles around it. The left wing houses the parish office and the adoration chapel, while the convention hall is located in the right wing. The original statue of the Immaculate Conception, which was placed in the main altar of the old church, can be seen at the parish office.
