At the center is the escutcheon of the family of St. Ignatius de Loyola, founder of the Society of Jesus. The right panel of the shield shows two wolves on either side of a cauldron, symbolizing the generosity of the Loyola family. On the left panel are the seven red bars on a field of gold, honoring the seven heroes of the family who distinguished themselves in a battle in 1301. This shield is part of the seal of most Jesuit schools in the world, with which the Ateneo shares a four hundred year old tradition of Jesuit education. 

Above the escutcheon, against a blue sky, is the golden crown of Mary, Mother of God, patroness of Bikol under the title of Lady of Peñafrancia. Arranged in a semi-circle under the shield are six golden stars representing the six provinces of Bikol. 

Over Mary's crown shines the sun, symbol of Jesus Christ. On its face is the seal of the Society of Jesus in calligraphic form: the first three letters in Greek (IHS) of the holy name of Jesus with the cross on top and the nails of the cross underneath. The sun's rays shine over Mary's crown, the Loyola shield, and the six stars, indicating that for Mary, the Ateneo and Bikol, Christ is the Light and the Life. 

The school motto inscribed on the upper rim, PRIMUM REGNUM DEI, "First the Kingdom of God" (Mt 6:33), expresses the single-mindedness with which the Ateneo de Naga must pursue the goals of Jesuit education.