Man-made mounds, höyüks in Turkish, are scattered across central and eastern Anatolia. Although the early periods have been excavated and documented, their medieval contexts have received minimal attention from archaeologists. As well, many höyüks were excavated as salvage excavations, and, when attention was paid to the medieval material, scholars focused primarily on the fortifications of these settlements. This has led to large gaps in our understanding of the occupants of these sites and their own perception and negotiation of settlement identity. In this paper I explore why these sites have been traditionally understudied and undervalued in medieval Byzantine scholarship. I review the methods used from past excavations that have created overly simplistic narratives and identities for these fortified settlements located on höyük mounds, generally with little regard for their surrounding environment and landscape. I argue against the use of definitional dichotomies, such as urban and rural, as analytical tools since they prioritize large settlements, and their material culture, over small, often rural, settlements, to represent imperial narratives as a whole. Instead, I propose the use of Queer theory to disrupt the use of heteronormative methods and binary analytical categories in order to produce a more inclusive narrative that incorporates höyük sites, and their medieval contexts, into Byzantine discourse. Three case studies are presented in this study (Taşkun Kale, Gritille Höyük, and Çadır Höyük), to demonstrate the multiple identities and functions associated with these sites on both local and regional scales. The goal of the paper is to highlight the importance of medieval settlements located at höyük sites in the complex networks of Byzantine Anatolia.