In Southwest Asia, fascinating changes in site use arose alongside the development of agricultural subsistence practices. This included the presence of more invested site features and locales used primarily for ritual activities. By the Pre-Pottery Neolithic period, more organized site use is reflected in the discrete middens evidenced at diverse types of sites, including Kfar HaHoresh (10,600–8,700 cal. BP)—the only Pre-Pottery Neolithic B site in the southern Levant that served a primarily ceremonial function. Contextual taphonomic analysis of faunal remains from midden areas at Kfar HaHoresh highlight an array of refuse deposition practices. This paper presents a comparison of animal selection, use, and subsequent deposition of remains in two middens at Kfar HaHoresh. Closer examination of the individual deposits that formed each midden reveals a more nuanced picture of how a ritualized space was organized across the Early, Middle and Late Pre-Pottery Neolithic B periods. Through combined analysis of social and spatial aspects of faunal contexts, this study highlights that ways in which wider regional changes in diet and disposal practices manifested in different ways at a ceremonial site.