Historians have long debated the role of climate in the rise and fall of empires of the 1st millennium CE. Drastic territorial contraction of the Byzantine Empire, societal decline, and beginning of the European Middle Ages have generally been linked to the Islamic conquests of the seventh century. This multidisciplinary archaeological investigation of trash mounds in the Negev Desert establishes the end date of organized trash management in the Byzantine-period city of Elusa and demonstrates urban collapse a century before the Islamic transition. Our findings, taken together with other evidence for Byzantine urban dysfunction, the Justinianic Plague, and recent research on the Late Antique Little Ice Age, flesh out the impact of the sixth century on broad historical trajectories.The historic event of the Late Antique Little Ice Age (LALIA) was recently identified in dozens of natural and geological climate proxies of the northern hemisphere. Although this climatic downturn was proposed as a major cause for pandemic and extensive societal upheavals in the sixth–seventh centuries CE, archaeological evidence for the magnitude of societal response to this event is sparse. This study uses ancient trash mounds as a type of proxy for identifying societal crisis in the urban domain, and employs multidisciplinary investigations to establish the terminal date of organized trash collection and high-level municipal functioning on a city-wide scale. Survey, excavation, sediment analysis, and geographic information system assessment of mound volume were conducted on a series of mounds surrounding the Byzantine urban settlement of Elusa in the Negev Desert. These reveal the massive collection and dumping of domestic and construction waste over time on the city edges. Carbon dating of charred seeds and charcoal fragments combined with ceramic analysis establish the end date of orchestrated trash removal near the mid-sixth century, coinciding closely with the beginning of the LALIA event and outbreak of the Justinian Plague in the year 541. This evidence for societal decline during the sixth century ties with other arguments for urban dysfunction across the Byzantine Levant at this time. We demonstrate the utility of trash mounds as sensitive proxies of social response and unravel the time–space dynamics of urban collapse, suggesting diminished resilience to rapid climate change in the frontier Negev region of the empire.