The Charities Regulator has asked the High Court to wind up the Inner City Helping Homeless (ICHH) charity.
The court has appointed Kieran Wallace of KPMG as provisional liquidator, and a hearing of a petition is set for November 1st.
The regulator says: "The responsibility for the administration and management of a charity at all times rests with its trustees.
"In circumstances such as those arising in the case of ICHH, this includes responsibility for proposing and implementing an effective and timely resolution to the crisis facing the charity."
It says its decision to present a winding-up petition "has not been taken lightly."
"It is a decision of last resort in circumstances where the charity's trustees have ultimately been unable to address the pressing need for stability and certainty for ICHH staff, volunteers and service users", it adds.
The charity found itself in the spotlight amid allegations of sexual assault against its founder.
Former CEO and Independent Dublin City Councillor Anthony Flynn died in August, while the complaints were being investigated.
The Charities Regulator says it first received a formal concern in late July.
It says this was immediately referred to An Garda Síochána, and the ICHH board was also contacted on July 30th.
Contact is ongoing with the charity's board of trustees, it adds.
