Hunter-gatherer architectural practices are one of the main sources of data to understand the complex land use of these societies. In the hyperarid Atacama Desert coast (Northern Chile), hunter-gatherers-fishers developed standardized stone-built architecture during the Late Archaic period (similar to 5,700-4,000 cal years BP), interpreted so far as sedentary villages or long-term campsites. Nevertheless, the lack of site formation process studies and systematic chronostratigraphies defy such functional interpretations. To address these issues, we reconstruct the lifecycle of a recently discovered semisubterranean structure at the Zapatero site (similar to 25 degrees S, Taltal). Combining stratigraphy, micromorphology, faunal and lithic analysis, as well as radiocarbon dating, we evidence a broad sequence involving different processes: shell midden formation; a stone-structure; a prepared burial pit; a burning event; a short-term occupational episode; and the entombment of the structure. We interpret this sequence as ritualized actions related to commemorative and place-making activities. Our work stresses the need for new research programs at the Atacama Desert coast, based on geoarchaeological approaches, to understand hunter-gatherer-fisher middening and architectural practices from the very materiality involved in stratigraphy-making processes.