Citipointe Christian College's controversial enrolment contracts are the subject of discrimination complaints to be filed with the Queensland Human Rights Commission.
The Brisbane school made national headlines this year over the contracts, which said it would only enrol students on the basis of the gender that corresponds to their biological sex.
It also said homosexuality is "sinful", like bestiality, incest and pedophilia.
The school eventually withdrew the contracts and principal Brian Mulheran stood aside in February.
Now parents and former students are aiming to create lasting change through the state's Human Rights Commission.
"I had no choice but to remove my children from Citipointe as I would not sign a contract that supported discrimination against my own child and other LBGTIQ+ children," Janina Leo, the mother of a former student said.
Fellow Citipointe parent Elise Myers has chosen to keep two of her children at the school as she waits to see how it will respond.
"I was in disbelief that a school would be able to do this ... I was just shocked that they would have the audacity," she said.
The complaints are being supported by the Queensland LGBTI+ Legal Service, which said it was important the process went ahead after the contracts were withdrawn.
"An act of discrimination is still an act of discrimination, if you break the law you do have to suffer consequences," the service's Matilda Alexander said.
"There has been nothing that has changed since that contract was withdrawn to make those students at that school or those parents feel safe."
By taking this action, her clients are hoping to prevent future cases of discrimination.
"A very clear way that we can do that is through implementing a policy at Citipointe that provides for respectful treatment of LGBTI+ students," Ms Alexander said.
A copy of the complaint will now be provided by the Human Rights Commission to the college, and the parties will be invited to participate in an early resolution process.
If it can't be resolved, it will be referred to the Queensland Civil and Administrative Tribunal for a binding determination.
The legal service expects to file more complaints in coming weeks and says it has been in contact with over 20 people about the issue.
Citipointe has been contacted for comment.
