Manuel Delgado quit his post on Tuesday night after a series of cases of reported mismanagement of funds at a charity set up for people suffering from rare diseases.
He will be replaced by Rosa Zorrinho in the position.
Paula Brito e Costa, who was at the helm of the charity, has also handed in her resignation. She is at the centre of the controversy, and is accused of misappropriating funds from the charity to buy clothes and cover personal expenses.
She quit three days after a TVI documentary into her management of Raríssimas was aired.
The investigation showed alleged mismanagement by Paula Brito e Costa, who apparently had used charity money to buy clothes and cover personal expenses.
“My presence is affecting the institution and I have to leave”, but she did not leave without a quip that she was the victim of a “perfectly laid plot”, Paula Brito e Costa told reporters earlier this week.
It was further revealed that Paula Brito e Costa received a base salary of 3,000 euros a month, excluding expenses and travel costs. A decree in 2014 had said that those leading charitable organisations should not be paid more than 1,685 euros a month.
Confronted with these facts, the outgoing Raríssimas chairman said her wage was fully justified and within the parameters of the law.