He became pope at a time of conflict between the newly dominant Christians and the pagan establishment in Alexandria, each of which was supported by a segment of the Alexandrian populace.

Scholasticus goes on to state that: Seizing this opportunity, Theophilus exerted himself to the utmost ... he caused the Mithraeum to be cleaned out ... Then he destroyed the Serapeum ... and he had the phalli of Priapus carried through the midst of the forum.

... the heathen temples ... were therefore razed to the ground, and the images of their gods molten into pots and other convenient utensils for the use of the Alexandrian church[3]The destruction of the Serapeum was seen by many ancient and modern authors as representative of the triumph of Christianity over other religions.

[citation needed] On 10 July in the Eastern (Greek) Orthodox Synaxarion, there is a commemoration for the 10,000 monks slain on the orders of Pope Theophilus in his paranoid campaign against perceived Origenism and the Four Tall Brethren.

His nephew and dynastic successor Cyril was canonized in both Eastern and Western Christendom, with the notable exception of the Assyrian Church of the East, for his articulation and defense of the hypostatic union, his central role at the First Council of Ephesus, and his opposition to Patriarch Nestorius of Constantinople.