The Charities Regulatory Authority has appointed inspectors to carry out a statutory investigation into the Gay and Lesbian Equality Network.
Glen announced last week it will close following a review of its operations.
The CRA emphasised that the opening of a statutory investigation is not in itself a finding of any wrongdoing.
It is the second inspection to be undertaken by the watchdog since it was given powers to investigate entities last September.
The CRA said the scope of the investigation will include the administration, governance and financial management of the charity by Glen's trustees and whether charitable assets have been used exclusively for charitable purposes and can be accounted for.
Early last month the regulator directed Glen's board to provide a number of documents.
In its statement the watchdog said that, having examined the documents, and after examining additional documentation received from the charity, it has determined that a statutory investigation into Glen is warranted.
The CRA also said it publishes investigations' reports on their completion.
In a statement, Glen said: "We acknowledge today's announcement from the Charities Regulator and wish to confirm that we will continue to work closely with the Regulator in this regard.
"We will not be making any further media comment until the Regulator's process is complete."
Last month, a report commissioned by Glen from Senator Jillian Van Turnhout found there was "mismanagement and poor practice" at the charity.
However, she said that there was no evidence of "material gain or misappropriation of funds".
