The Celali rebel armies ravaged the central Anatolian countryside from the late 16th up to the mid-17th century. The Celali movements brought about demographic changes and had a long-lasting impact on agricultural economy in some regions. Anatolian waqf institutions being dependent on rural taxpayers and agricultural production for their budgets were seriously harmed by the Celali rebellions. This paper examines the Celali effect through the Waqf of Hatuniyye which had villages scattered across central Anatolian districts. The waqf fell into a deep financial crisis and its regular functioning was disrupted in the early 17th century. The waqf finance was unable to recover for decades after the crisis, which indicates that rural economy in waqf villages suffered from a perpetual production and population crisis.