Teddy Hope, who held a high-profile position as a trans officer in the Out For Indy wing of the party before their resignation, told The Herald on Tuesday that the SNP leadership had failed to protect the trans community.
It comes after Teddy, who is non-binary and uses the pronouns “they” and “them”, was verbally abused at a branch meeting of the party while discussing transgender rights.
According to the Herald, minutes of the meeting recorded that non-branch members attended the gathering and “appeared to be bent on confrontation.”
"At one point photocopies of men taken from the internet were passed with the comments that they had all been convicted of predatory and paedophilic behaviour against women and girls while self-identifying as women,” the minutes add.
“There were also shouted comments of men getting access to women/girls in toilets and changing rooms and raping them and the infiltration of LGBTi information in primary schools encouraging children to identify as gay or trans.”
“The atmosphere was such that the convenor ended this part of the meeting and asked all of those who were non-members to leave.
“The secretary accompanied the guest speakers out of the room and apologised to them for what had happened.”
After Teddy wrote about the abuse on social media, Angus MacLeod, the then-National Secretary of the SNP, initially asked them for details.
But Teddy alleges that Mr Macleod stopped corresponding in August, and added that no action has since been taken by the party over the abuse.
“My friends have been complaining about transphobic abuse in the party for years,” Teddy said, “and just haven’t been getting any feedback or response from the party.
“So the fact that headquarters, the National Secretary, finally was willing to listen to my complaint and seemed to be taking it seriously was a big deal.
“I felt like they were going to start taking the issue of transphobia seriously.
“I sent all the information and he said he was investigating, but he just faded out.
“I tried emailing and he didn't respond.”
Teddy has since contacted Stewart Stevenson MSP, the new National Secretary, about the abuse but has not received a response.
“To be completely honest,” Teddy said, “I think the SNP is now one of the core hubs of transphobia in Scotland.
“It needs to be accountable for its actions and harms it is doing to the trans community. I don't think the party is at all safe for trans people.
“I can probably count the number of trans people I know who are still active and public-facing in the party on one hand.
“We all share this deep fear of being abused or being stalked and harassed, and it's terrifying.”
Teddy has now called for the extent of transphobia in the party, as well as the lack of action on complaints, to be investigated.
They said: “I think what we need now from the SNP, at the very least, is a public apology from the leadership from towards the trans community for what they've done.
“They need to promise to make the party safe by bringing in a workable definition of transphobia as soon as possible, or else the party will just continue to harm trans people both externally and internally.”
A spokesperson for the SNP said Mr Stevenson was still investigating Teddy’s case.
“The SNP has a proud record on equalities issues, we treat all complaints seriously and we regret to hear of negative experiences of this nature,” they said.
"There is no room for transphobia in the SNP and no room for transphobia in Scotland - and our new National Secretary is continuing to investigate this case."
Reacting to the news of Teddy’s resignation, John Nicolson MP told The Scotsman that the concerns of trans people in the party “should be taken absolutely seriously” and added that the SNP must not be seen to be “half-hearted” over its championing of trans rights.
He called the abuse suffered by Teddy “absolutely appalling” and said their complaint must be investigated thoroughly.
The MP for Ochil and South Perthshire, who is gay, said all political parties had problems with transphobia “to a degree” but insisted that the “vast majority” of SNP members - particularly young people - were supportive of LGBT rights.
Instead, he blamed the clash over trans rights on a small “hard core of obsessives online”, who “peddled sinister claims” about the trans community.
“I think for the vast majority of members this issue is not on their radar at all.”
The 59-year-old, who is running to be the Rector of Glasgow University, called the fight for trans rights “the Clause 28 of this generation.”
“It has many of the same myths that were spread about gay people being recycled - particularly the obsession with toilets and trans people as predators.
“The tragic fact is that it is far too easy for women to be abused without the predator going to the trouble of changing their gender.
“This stuff just does not stand up to scrutiny.”
“Scotland has gained a wonderful reputation for welcoming LGBT people,” he added, “but I do think we have to be vigilant.”