St. Mary's Church in Maynooth contains within it the bones of a much older building, and the join between old and new is visible to anyone who looks carefully at the eastern tower. The crenellations along the top are modern additions, but below them the masonry tells a different story. Four late medieval windows punctuate the east wall, and the north wall carries a row of slit opes, the narrow vertical openings common in medieval stonework, designed to admit light while offering minimal exposure to the elements or to attack. The tower also has a basal batter, meaning its walls angle slightly outward at the base, a technique used in medieval construction to add structural stability and to make undermining more difficult.

This tower belonged to an earlier, manorial church, one that was directly associated with nearby Maynooth Castle. Manorial churches of this kind were private foundations tied to the local lordship rather than to a parish community in the ordinary sense, and their architecture often reflected the status and ambitions of the lord who built or patronised them. The Fitzgeralds, Earls of Kildare, were the dominant force in Maynooth from the medieval period, and the castle itself was one of the most significant seats of power in late medieval Ireland. The church would have stood in close relation to that world. On the western side of the tower, two round-headed openings are still visible, though both are now blocked. These were probably doorways connecting the tower to an upper storey of the original church, a feature that suggests the building had some vertical complexity, perhaps a gallery or elevated chancel arrangement, now entirely lost.