In this article, we explore transformations and continuities in cosmology and cultural landscape structure across Pueblo history in the US Southwest. Many researchers have directly compared the archaeology of the society centered at Chaco Canyon (ca. AD 850–1140) in northwestern New Mexico with ethnographic documentation of Pueblo communities from the nineteenth and twentieth centuries. This approach makes it difficult to understand how cultural transformation played out in the intervening centuries. Here, we investigate this history by comparing Kin Nizhoni, a Chaco-era Great House community in the Red Mesa Valley, with Wiyo’owingeh, a post-Chacoan community in the Rio Grande Valley. We find that the built environments of both sites expressed similar cosmological principles, but architectural expressions of these concepts became less explicitly marked over time. We also find that this similar cosmology was mapped onto different social structures, with a focus on elite architecture in the Chaco era as opposed to communal dwellings with spatially separated shrines in later Pueblo contexts. We close by proposing a connection between the functions of Chacoan Great Houses and later Pueblo World Quarter Shrines. Overall, our findings underscore the utility of cultural landscape studies for tracing relationships between religion and society across North American Indigenous histories.