Beneath the stone keep of Maynooth Castle lies a sequence of occupation that pre-dates the castle itself by centuries, possibly millennia. 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, found not one settlement but seven distinct phases of human activity layered one atop the other. The earliest was a rectangular prehistoric building, leaving almost no finds of its own, though a stone axe head and an unfinished macehead recovered nearby may have originally belonged to it.

Above those prehistoric traces, at least two small round houses were built, each roughly five metres across and constructed using post-and-wattle, a technique in which upright wooden posts are woven with flexible rods to form walls, typically then plastered with daub. Both are thought to be early medieval in date, somewhere in the first millennium AD, and while no datable objects came from them, good carbon samples were retrieved from their hearths and post-holes. The later of the two round houses appears to have had a curving wooden stockade built against one side of it, and it seems to have been in use at the same time as the surrounding land was first being cultivated, with regularly spaced shallow furrows surviving in the soil. That farming activity eventually spread over the house itself and continued until around 1175, when the site passed into Norman hands. The newcomers raised a sod mound roughly a metre high and built a rectangular post-and-wattle structure on top of it, enclosed by a wooden fence with an entrance facing east. Finds from this layer included an arrowhead, an iron spur, a scabbard chape, and pottery identified as Ham Green ware, a type produced near Bristol and commonly associated with early Anglo-Norman settlements in Ireland. Within little more than a decade, probably in the late 1180s, the stone keep was under construction, its progress recorded in the thick mortar slicks that still survived across the site.

The keep itself is open to visitors as part of Maynooth Castle, and the ground-floor exhibition space whose development prompted the 1996 excavation offers some context for the site's long history. The early medieval round houses and the layers beneath the Norman masonry are no longer visible, but knowing they exist, compacted into the ground underfoot, gives the castle a different kind of depth.