The edifice's massive triangular structure symbolizes the Holy Trinity, as well as the three-fold mission and vision of the school.

Its shape and design are also meant to suggest the outstretched arms of the Sacred Heart, and the traditional Filipino bahay kubo (nipa hut).

One side of the church houses a chapel dedicated to the Virgin Mary as the Immaculate Conception, patroness of Ateneo de Manila and of the Philippines, while another side chapel is dedicated to the Sacred Heart of Jesus, a devotion committed to the Jesuits by Jesus's appearances to Saint Margaret Mary Alacoque at a convent in Paray-le-Monial in 1671.

However, only the Blue Eagle Gym (located near the Grade School) stood, having been the first structure built in what would eventually be Loyola Heights.

The stoup itself is an upright brownstone, with a depression on top acting as the basin and the outlet for the water covered with a clay plate with the Jesuit seal.

The altar is supported by a slab of adobe rock, believed to be in abundant supply underneath the Loyola Heights campus.