The motto of the school is ''In Omnibus Amare et Servire'' ("To Love and Serve in All Things") which was taken from the Spiritual Exercises of St. Ignatius of Loyola.

The school seal holds the school’s coat of arms (shield), the insignia of the Society of Jesus, and the school’s motto.

The shield rests on the seal’s field of bleu celeste (sky blue). It is divided chief per pale, that is, the field is cut vertically in the middle with a running band across the top. It is tinctured with the colors of the Philippine flag. The chief (the top band) is in azure (blue) on which the superimposed capital letters ‘AM’ (Ave Maria) are emblazoned en blanc—in white. Blue and white are the traditional colors associated with the Blessed Virgin Mary, to whom the school is dedicated from the beginning. Likewise, all Ateneo schools are identified by the same colors. The dexter (right) side of the shield is a white field which holds two black wolves and a pot, the lobos y olla. A wolf is a device for nobility, the kettle a symbol of generosity. It is the traditional symbol for the House of Loyola, from which the founder of the Jesuits came from.

The sinister (left) side of the shield is a golden castle on a red field. The device is based on the central design of the official seal of Iloilo City. It is reminiscent of Fort San Pedro, the stone bastion that used to guard the entrance of the city’s port.

Crowning the shield is the official insignia of the Society of Jesus. It is a simple orb with three capital letters – I H S: the first three letters of the name of Jesus in Greek (iota, eta, sigma). On the eta stands the Cross; below the letters are the three nails of the Crucifixion. Emanating from the Christogram are rays of light, symbolizing Christ as the Light of the world whose teachings should illumine all mankind.

Supporting the shield are the Chinese characters for the Blessed Mother. They likewise remind its bearers of the Chinese roots and identity of the institution.

Beneath is the school’s motto: In Omnibus Amare et Servire (To Love and Serve in All Things). The motto is from the Spiritual Exercises of St. Ignatius of Loyola, expressing the Ignatian ideal of loving and serving Jesus Christ and one’s fellowmen.

The entire seal is enclosed with white scrolls bearing the appellations of the school. On top is its official name, in capitals, ATENEO DE ILOILO; beneath is its founding name, Santa Maria Catholic School.

The seal next (right) is the former seal of Santa Maria Cetholic School that was used from 1958 until 2004 with the Motto "Ora et Labora" which means Pray and Work, viewing the two as partners, and believing in combining contemplation with action.