Recent geophysical surveys at six sites in the Illinois River Valley (IRV), just north of the Greater Cahokia area, provide new insights into the region’s volatile era of Mississippian occupation by revealing a series of important changes in community organization that occurred from the eleventh to fifteenth centuries. Geophysical data allow us to evaluate these changes through the lens of site layout, special-purpose architecture and communal space, and the spatial alignment of site features to consider how the construction of Mississippian spaces structured social organization and identities. When considered in conjunction with data from previous excavations in the region, this geophysical work indicates that religion played a key role in forging new relationships and shared identities among early Mississippian IRV and Cahokian groups. Our analysis also reveals that IRV Mississippians reconfigured important aspects of these religious practices and socio-political relationships in the context of warfare-induced population nucleation beginning around 1200 CE, leading to more locally structured identities over time.