The founder of a website that collected donations for city charities mysteriously disappeared and shuttered her company — making off with thousands of dollars, a new lawsuit alleges.

Starting in May, NYCharities.org, Inc., “had begun functioning like a Ponzi scheme … all the while compensating its now-disappeared founder and president, and struggling to hide its misuse of the funds entrusted to it,” charges the Manhattan Supreme Court lawsuit filed late Friday by nonprofit Ice Theatre of New York.

Ice Theatre — an ice-skating dance company with a yearly budget of just $300,000 — says it used the website to collect donations and first caught a glimpse that things weren’t right on June 28 when a donor’s contribution wouldn’t go through.

After leaving several voicemails and emails for founder Cristine Cronin, Ice Theatre executive director Jirina Ribbens finally reached Cronin, who said NYCharities was “aware of the problem” and was working to fix it, according to the court papers.

But “Cronin never called Ribbens that afternoon. Indeed, Cronin never called Ribbens again,” the court documents claim.

Within a few days, NYCharities’ office space was closed and Cronin stopped answering calls or returning emails from Ice Theatre — which NYCharities still owes about $10,000 in donations from May and June, court papers claim.

The website — which was founded by Cronin in 2004 — went back up for a few days in July before the Attorney General’s Office shut it down Aug. 2 amid an investigation.

Over the last several years, board members had resigned from NYCharities, which “began to deteriorate as a result of the actions and inaccuracies of management and directors of NYCharities,” the lawsuit says.

“NYCharities thus concealed from ITNY the increasing peril confronting the funds that NYCharities held and accumulated as agent-fiduciary of ITNY.”

The suit says the website usually made payouts to the charities in bulk monthly rather than as the donations came in. And when it got into financial trouble, the website started using new donations to pay charities it already owed money to, the court papers say.

Attorney General Letitia James announced at the end of July that her office was investigating NYCharities. The investigation is ongoing, the office confirmed.

“NYCharities.org is inexcusably depriving charities of their donors’ generosity,” James said in a statement at the time. “Leaving New York’s charitable organizations high and dry by denying them what they are owed is unacceptable.”

Another nonprofit dedicated to preserving architecture in an uptown neighborhood, Friends of the Upper East Side Historic Districts, lost over $10,000 in donations when the website closed, according to the president Franny Eberhart, who said donors were able to recoup much of the money from their banks.

“It was a tremendous shock,” Eberhart said adding the situation reminds her of a small-time Bernie Madoff.

“I sure hope they find that person,” Eberhart said of Cronin.

Owen Foote, the Treasurer of Gowanus Dredgers — a non-profit that helps to raise awareness about improving the Gowanus Canal through canoeing and kayaking — said his organization lost $1,000 and lost a platform for competitive fundraising.

“We are very small not-for-profit and we don’t really have any resources to go after them so we hope the Attorney General’s effort to reclaim these funds on our behalf is successful because $1,000 or $2,000 dollars is significant when you are reliant on volunteers and small donors,” Foote said.

A working number could not be found for Cronin. A message left on NYCharities’ Facebook page was not immediately returned.