The Peter McVerry Trust has confirmed that the CEO Francis Doherty tendered his resignation to the board of directors this morning.
In a statement, it expressed disappointment with Mr Doherty's decision, but wished him well after what it described as "a difficult period for him".
The charity said that its focus remains on the future of the organisation.
"We will co-operate with all stakeholders to achieve that as best as possible. Continuity of care for our participant group remains our priority," it added.
Last month, the State's regulator for housing bodies appointed inspectors to carry out a statutory investigation into the Peter McVerry Trust.
The Approved Housing Bodies Regulatory Authority (AHBRA) said it was first notified of a number of financial and governance issues at the housing charity in July.
AHBRA said it had determined that a statutory investigation was required having identified concerns in relation to the organisation.
An independent auditor was appointed to carry out a financial and governance review during the summer after the charity said it was facing serious cash flow pressures.
The Irish Times has reported that Mr Doherty, who took over as head of the trust in June, stated in his resignation letter, that he felt the board of the charity had made his position "untenable".
