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The CEO of a tax-payer funded nonprofit that serves some of the city’s neediest city populations bilked the organization out more than half a million dollars to fund lavish vacations and high-end dinners, prosecutors said.

Reginald Williams, 67, allegedly hatched a series of schemes to rip off the the Addicts Rehabilitation Center Foundation, which he ran, and a related group called the Addicts Rehabilitation Center Fund. Both groups provide social services and housing to drug addicts and those living with HIV and AIDS.

Williams is also the longtime pastor of the Charity Baptist Church in the South Bronx.

Williams also enlisted the help of co-defendants Naomi Barrera, 42, the current president and CEO of the ARC Foundation, and Bennie Hadnott, 74, a financial consultant, to pull off the schemes.

The thefts occurred when Williams was president and CEO of the ARC Fund and later the chairman of the board of the ARC Foundation — both of which are cash-strapped organizations who contract with the city and state to provide essential services.

“Even while their organizations struggled financially – failing to meet contractual obligations and even furloughing employees without pay – these defendants continued to drain the coffers for their personal gain,” said Manhattan DA Cyrus Vance Jr. in a statement.

In total, the Bronx pastor netted $631,271 that he spent on monthly jaunts to the Bahamas, Jamaica and the Dominican Republic for friends and family and extravagant dinners and bar tabs, according to prosecutors.

He allegedly claimed the personal expenditures were business expenses and submitted receipts for reimbursement. Prosecutors say that he submitted the same invoices to both the ARC Foundation and the ARC Fund so he’d get reimbursed twice.

In another alleged scheme, the ARC Foundation paid Hadnott’s consulting firm $200,000 between 2010 to 2015. In return, Hadnott paid a 25 percent kickback directly to Williams.

In another money grab, Williams and Barrera allegedly pocketed cash from the sale of an ARC foundation property and from loans intended to benefit the organization.

The trio pleaded not guilty Wednesday in Manhattan Supreme Court to grand larceny and other charges. They were released without bail. After the hearing, Williams and his co-defendants declined to comment.

Prosecutors said that Williams misconduct and abuse of his position stretched back many years prior to the charged crimes.

The indictment was the product of a joint investigation by the Manhattan DA, the city’s Department of Investigation and New York’s Inspector General.