Interior painting was made by Italian artist Giacomo Lattanzi, who painted walls, columns and ceilings with characteristic light blue, pink and golden colors. Ribs decorate and give structure to vaults with beautiful natural elements forming garlands covering them entirely. Ornamentation was completed by several artists, such as painter Onofre Jarpa, who was in charge of altar and reredos decoration; and sculptor Virginio Arias, who created bronze pieces.

One of the most important and admired interior works is the set of stained glass windows on the walls by the famous German Munich-based stained glass design and manufacturing company Franz Mayer & Co., a company whose artwork is displayed in other churches in Santiago. The basilica has 26 pointed-arch stained glass windows, some of which shattered during 1985 and 2010 earthquakes:

The first 11-piece stained glass series, located in the central altar and adjacent areas, represents Catholic Church saints and images, namely:

– Saint Matthew
– Saint Mark
– Sacred Heart of Jesus
– Saint Luke
– Saint John
– Saint Andrew
– Immaculate Conception
– Saint Paul
– Saint Francis de Sales
– Christ the Redeemer
– Saint James

The second series is composed of 14 stained glass windows along lateral naves and transept, which different events in the life of Jesus Christ. Left lateral nave displays:

– The Annunciation: the angel Gabriel visits the Virgin Mary and tells her that she would conceive and become the mother of Jesus, the Son of God.
– Baby Jesus is visited by the Wise Men. (Transept): Melchior, Caspar and Balthazar visit Jesus after his birth, bearing gifts of gold, frankincense and myrrh.
– Presentation of Jesus at the Temple: Mary and Joseph follow a priest holding Infant Jesus, who presents him at the temple.
– Flight into Egypt: the Holy Family flees after learning that King Herod intended to kill the infants of that area.
– The Holy Family: Joseph, Mary, Saint Anne and Saint Joachim surround Infant Jesus within the home.
– Christ among the Doctors: it represents an event during the early life of Jesus, when he is found in The Temple in deep discussion with five elders.
– The baptism of Jesus by John the Baptist: It portrays Jesus being baptized by John on the bank of the Jordan River, and the Holy Spirit descending as a dove towards Jesus, which consecrates him as the Christ.
Right nave depicts the following biblical scenes:
– The temptation of Christ: It portrays Jesus refusing each temptation by the devil during the forty days and nights that Jesus spent in the desert preparing himself for his Ministry.
– Let the little children come to me: Jesus is surrounded by children, representing the love for the innocence and purity of childhood.
– The cleansing of the Temple: An angry Jesus expels the merchants and money changers from the Temple, accusing them of turning the consecrated Temple into «a den of thieves» through their commercial activities.
– Render unto Caesar the things that are Caesar’s, and unto God the things that are God’s: Jesus answers a provocative question asked by a Pharisee of whether it was lawful for Jews to pay taxes to Caesar.
– The Last Supper: During the meal Jesus shares with his Apostles, he predicts the betrayal by one of the Apostles present, while they wondered who this person would be.
– Christ Crucified. (Transept): Jesus, after being arrested and scourged, is nailed to a cross, where he dies some hours later.
– Jesus appears to the Disciples: It portrays the second appearance of Jesus to his astonished and marveled Apostles, along with the Virgin Mary, displaying his wounds to an incredulous Saint Thomas, who is on his knees.

A single stained glass window on the entrance porch: It depicts an illustrated scene where Archbishop Mariano Casanova offers, along with other religious, the just-finished temple to God.