In the interior of the Church of Saint Philomena there are fasciculate columns and is decorated with marble-type paint.

The interior of the entrance door is decorated in a Gothic portal style, with archivolts that form successive growing ogival pointed arches. The decoration continues with golden paint on the walls with different symbolic motifs, including a monogram of Saint Philomena. The upper finishing touch of this portal is a set of ribs pictorially decorated that ornament its union with the upper layout.

The central nave is higher than the lateral ones and is finished off in a ribbed vault, from which hang five hexagonal lamps. The upper part is finished off with stained-glass windows. The motifs of the stained-glass windows of this nave are religious and curiously they are inscribed with the names of the donors. From south to north, on the left: Ms. Loreto Cousiño de Lyon, Villaseca Ossa, Ms. Olea, Paulina Clunes and Isidora Lyon. On the right: Ricardo Lyon Pérez, Carlos Cousiño Goyenechea, Círculo Social del Patronato, Saint Philomena, Juan Nazar and Adriana Cousiño and Instituto Juan Pablo. In all the walls are abundantly decorated and painted with organic motifs linked to crosses and religious symbols. The colors used in the ornaments are mainly light blue and gold over a brown background.

There is a similar decoration in the transept. However, the stained glass windows that crown the top part are based on the themes extracted from the life of Saint Philomena and topped on both sides by a ceiling rose. The set of stained glass windows related to Saint Philomena are nine and they are not placed in an exact chronological order, which show more important passages in the life of the Saint. These were made in the workshop of Félix Gaudin and arrived to Santiago in 1905. They are neo-Gothic in style, their formats are vertically topped in ogival pointed arches and the technique used is painted and furnace-heated glass.

The high altar is located in the apse of the central nave and people can walk about through its back part. It has a gilded Gothic-style shrine with a rather high pinnacle somewhat similar to the Gothic European cathedrals. The Holy Sacrament is kept within this shrine.

In order to understand the scenes portrayed in the stained glass windows it is necessary to be familiar with the history of Saint Philomena. Her parents were imprisoned by their suffering because they were unable to conceive children, until they were healed by a Roman doctor and thus embraced the Christian religion. They named their daughter Lúmen, light of the faith (Philomena), and brought her up with the best care they could give her. At age thirteen Philomena accompanied her father to Rome in order to establish a peace treaty with Emperor Diocletian on behalf of one of the small Greek countries existing at the time. The emperor offered the people peace and protection in exchange for Philomena. Although her father thought it was a good offer, he did not know that Philomena was already following the path of the Lord, refusing at all times to follow her parents’ wishes to get married. The emperor was in a rage and went on to torture her and put her in jail. After thirty-seven days in prison the Virgin Mary and the Holy Child appeared before her, telling her that in three days she would ascend to heaven. Thus, Philomena was tied to rocks and thrown into the river, and was saved by two angels. Afterwards, she was tied to a tree trunk where she was to await her death by bow and arrows, but when the arrows were shot they turned around and killed the archers. On the third day she was ordered to be decapitated by the Emperor, complying with the deadline prophesized by the Virgin, which according to tradition, was on August 10th.

The scenes represented in the stained glass windows correspond to: The discovery of the tomb of Saint Philomena; The sentence dictated by the Emperor of throwing Saint Philomena into the river; The sentence to decapitate Saint Philomena: The sentence of killing her with bows and arrows; The ascension of Saint Philomena; The appearance of the Virgin with the Holy Child; Emperor Diocletian asking for Philomena’s hand in marriage; Philomena’s education and the Consecration of Saint Philomena.

The altars are located on both sides of the transept, decorated with architectonic motifs associated with the neo-Gothic style. To the right of the altar is the Crucifixion of Christ and the left side of the altar is dedicated to the Holy Virgin and Child.

In the lateral naves, built in ribbed vault, are the confessionals, made in wood and decorated with Gothic architectonic elements related to the general style of the temple, such as the altars. Thus, the observer can see figures dedicated to Saint Philomena, the Holy Virgin Mary and La Pieta.