The Virgin Mary is also viewed as the Ark of the Covenant because God dwelt within her. She also carried within her womb the creator of all things, and she herself became “the holy of holies.” This image is closely connected to the apocryphal story from the Protoevangelium of James, in which Joseph accuses Mary of adultery. Her close association with the temple was directly linked to the fact that in the Christian tradition Mary is viewed as the temple. While all Christians are in some sense the temple of the Holy Spirit when they bear the Word of God, Mary's role as a temple of the Holy Spirit was unique, because only she nourished Christ in her womb.

The fourth-century bishop of Alexandria, Athanasius, also wrote eloquently about the Virgin Mary, making strong connections between her and the Ark of the Covenant. He was an extremely influential writer, expressing many of the mysteries of the Incarnation in powerful, lucid terms. He wrote, “O [Ark of the New] Covenant, clothed with purity instead of gold! You are the Ark in which is found the golden vessel containing the true manna, that is, the flesh in which divinity resides. You surpass them, for it is written: ‘The Old Testament earth is my footstool' (Is 66:1). But you carry within you the feet, the head, and the entire body of the perfect God.”