Throughout the Angkor period (9th to 15th centuries CE), the Khmer kingdom maintained a series of interconnected cities and smaller settlements across its territory on mainland Southeast Asia. One such city was Koh Ker, which for a brief period in the 10th century CE even served as a royal capital. The complexity of the political landscape meant the Khmer kings and the elite were particularly mobile through the Angkor period, and rupture in royal houses was common. However, while the historical record chronicles the 10th century migration of the royal seat from Koh Ker back to Angkor, the fate of Koh Ker's domestic population has remained unknown. In this article, we reconstruct the settlement history of Koh Ker, using palaeoecological and geoarchaeological techniques, and show that human activity and land use persisted in the city for several centuries beyond the city's abandonment by the royal court. These results highlight the utility of multi-proxy environmental reconstructions of Khmer urban settlements for re-evaluating prevailing assumptions regarding the use and occupation of Angkor-period cities.