Tai Cantref said in a statement its chief executive Lynne Sacale had left the organisation after 10 years with the company.
It rents more than 1,400 homes in Ceredigion, Pembrokeshire, Carmarthenshire and Powys.
When the inquiry was announced last August, Tai Cantref said it was fully compliant with regulations.
A statement posted on its website stated: "Tai Cantref can confirm that its chief executive, Lynne Sacale, has left the employment of the organisation and we wish her every success in her future endeavours and would like to thank her for her hard work during her time with the company.
"Tai Cantref's number one priority is its tenants and ensuring the service and level of support provided on a day to day basis is of the highest possible quality.
"With that in mind, the board of Cantref will continue to receive support from Doug Elliot, previously head of regulation at the Welsh government and Hilary Jones, chief executive of Bro Myrddin Housing Association."
The head of a housing association under scrutiny from the Welsh government has left her post.