The charity watchdog will investigate the trust of a school which was previously criticised for segregating male and female staff.
Rabia Educational Trust, which runs Rabia School in Luton, is alleged to have breached Department for Education imposed operating conditions.
The Charity Commission said there had been evidence it admitted new pupils despite being banned from doing so.
The BBC has contacted the trust for comment.
The independent school, in Portland Road, was set up to provide an Islamic education and according to its accounts had 44 pupils in 2018-19.
In 2016, the then chief of Ofsted Sir Michael Wilshaw wrote to Education Secretary Nicky Morgan advising her that for the initial meeting with inspectors "the school insisted on segregating men and women through the use of a dividing screen across the middle of the room".
At a visit two years before that inspectors said the school was "undermining British values" and "limits girls to knitting and sewing" in technology classes.
The charity watchdog said it previously investigated the trust in 2016-17, "finding there had been misconduct and/or mismanagement" and issued the trustees with a legal order.
It added it had since kept the trust "under close review" and found trustees had "persistently failed in the requirement to meet the independent schools standards".
It said new pupils had been banned because of "successive safeguarding and welfare failings".
The watchdog said the fresh inquiry would "examine the trustees' compliance with their legal duties around the administration, governance and management of the charity, and whether the charity can be placed on a firmer footing for the future".