Syed Adnen Hussin wants to create a space where gay or transgender Muslims can be themselves while they pray — which he said doesn't happen at other mosques.
"It's not so much that they're not welcome, but they can't affirm that aspect of their identity," he said.
"You can be a queer but you can't affirm your identity when you're in a religious space like a mosque. So you couldn't, for example, be trans and decide that you wanted to pray on the women's side if you looked more male."
But Muslim scholars say the Qur'an is clear on homosexuality.
"What the Qur'an says clearly, just like the Bible, that homosexuality is not accepted," said Jamal Badawi, a professor emeritus at Saint Mary's University in Halifax.
"It is not regarded as the norm in terms of the needs of society and the relationship between men and women."
Badawi said people shouldn't misinterpret what he or the Qur'an says. He said Islam does not preach violence or hatred against gay or transgender people.
"There is a big difference between disagreement and discrimination. You can disagree with people and their views," he said.
"Everybody's entitled to the right to agree or disagree with anybody's ideas. But discrimination, that's what we all should be against."
Several imams in Halifax said everyone is welcome in the city's five mosques regardless of their sexual orientation. They told CBC News they have not heard of or met a gay or transgender Muslim in the city.
"All mosques, everybody is welcome in the mosque regardless of race, colour, gender, whatever," said Imam Ibrahim Alshanti, of the United Muslims of Halifax.
"To open a new mosque specially for these people, maybe it's not necessary."
No one has an accurate count of gay or transgender Muslims in Nova Scotia.
But Hussin said numbers aren't important — having a choice of where to pray openly is.
"To me, creating a spiritual space where all are equal is really important because that might impact their lives outside of the spiritual arena as well," he said.