The years of the late 16th into the 17th century were characterized by the harsh Celali rebellions and ensuing social turmoil in the central provinces of Anatolia. The years spanning 1603-1608 saw mass population movements called "The Great Flight". In fear of rebellions, villagers took refuge in safer locations, such as fortifications, mountain villages and sheltered in conglomerated villages. Some migrated to the western provinces far from the Celali movements. Life and earning the means to maintain that life were certainly difficult for the migrants but it could not have been easy for those who remained in their homelands as well, whether peasant or townsmen. Mass migrations and flights meant a loss of population, including laborers, cultivators and taxpayers. Thus, they brought about a food shortage for the remaining populace and revenue loss for the institutions which drew taxes mainly from the rural population and their products. Among these institutions which experienced financial difficulties in the wake of Celali movements were the waqfs. Since these charitable endowments were provisioning the towns, employing townsmen in various capacities, feeding and giving pecuniary aid to the needy and supporting economic and commercial life in town, their financial troubles affected and spread over the economic and social life of the entire town. Although the Celali rebels and bandits primarily plundered unguarded rural areas and let villagers flee, urban economies and commerce collapsed and living conditions deteriorated in the towns. As the regular functioning of waqf institutions ceased and they fell into financial distress due to mass migrations, the dire straits in daily life were further exacerbated for the townsmen. This paper looks at the effects of Celali-led migrations and flight for the Anatolian waqfs and shows that their effects persisted as some waqfs failed to recover or managed to recover only partially in the following decades.