A Bay Shore couple has been charged in federal court in Manhattan with fraud and embezzlement and misappropriating $953,875 from New York City through a nonprofit that operated senior centers.

Kwame Insaidoo, 59, and Roxanna Pearson, 62, allegedly stole the money from United Block Association, a nonprofit that has been paid more than $11.6 million since 2008 to operate and provide healthy meals at four upper Manhattan senior centers.

Insaidoo, the executive director, was accused of overbilling the city for supposed food purchase — claiming expenses 500 percent higher than actual expenses in some reports — while working with his wife to funnel money out through a shell corporation.

They allegedly used the proceeds of the scheme to pay the mortgage on their Long Island house as well as utility bills, the purchase of a luxury car, clothes and insurance.

Pearson had been a consultant to the nonprofit until 2012 when she was terminated under city anti-nepotism policies, but Insaidoo continued to authorize payments to her, the government said.

“Kwame Insaidoo and Roxanna Pearson allegedly diverted close to a million dollars in public funds designed to assist our city’s elderly, and spent it on themselves,” U.S. Attorney Preet Bharara said in a statement from his Manhattan office.

The two are expected to be presented in court Wednesday afternoon.