Beneath the floor of Maynooth Castle's great stone keep lies a sequence of occupation that long predates any Norman ambition in Kildare. When excavations were carried out in 1996, ahead of the conversion of the keep's ground floor into an exhibition space, archaeologists working for Dúchas, The Heritage Service, uncovered not one earlier settlement but seven distinct phases of use, stacked one upon another across an extraordinary span of time.

The earliest structure was a rectangular building of prehistoric date, its function and precise age uncertain, though a stone axe head, an unfinished macehead, and waste flakes of flint found nearby may be connected with it. Above those remains, probably during the early medieval period, at least two small round houses were built, each roughly five metres across and constructed using post-and-wattle technique, in which upright wooden posts are woven through with rods or branches and typically finished with a daub of clay or mud. No datable finds came from these houses, but carbon samples recovered from their hearths and post-holes offer the possibility of future dating. The later of the two houses appears to have had a curving wooden stockade added to one side, and it seems to have been in use at the same time the surrounding ground was first brought under cultivation, marked by regularly spaced shallow furrows. That cultivation eventually overtook the house itself and continued, according to the evidence, right up until the arrival of the Anglo-Normans. The site appears to have passed into Norman hands around 1175, at which point a low mound of sod, roughly a metre high, was raised, with a rectangular post-and-wattle building on top and a stout wooden fence enclosing the whole. Finds from this level included an arrowhead, an iron spur, a scabbard chape, and pottery identified as Ham Green ware, a Bristol-area product common on Anglo-Norman sites in Ireland. By the late 1180s, the first stone keep was under construction, its presence recorded in the excavation by thick mortar slicks. That original keep was divided internally into two rooms by three piers carrying the first floor, forming the foundation, in the most literal sense, of the structure that visitors can walk into today.