SNP leader Nicola Sturgeon and her Westminster counterpart Ian Blackford faced demands for the SNP whip to be removed from the Edinburgh South West MP.
The party has been dogged by infighting over transgender rights connected to the ongoing bitter public debate about reform to the Gender Recognition Act, something the SNP and the Scottish Greens have committed to progress in this parliamentary session.
Ms Cherry has been an outspoken critic of the SNP’s policies and on Monday was criticised by End Conversion Therapy Scotland for allegedly seeking to “justify conversion therapy”.
Out for Independence, the official LGBTQ+ wing of the SNP, broke ranks on Tuesday to call for Ms Cherry’s expulsion from the party.
The group tweeted: “Out for Independence calls for the removal of the SNP whip from Joanna Cherry MP and echoes @YSINational’s [Young Scots for Independence] calls for an independent investigation into transphobia in the party.”
The move was backed by SNP Students, which criticised Ms Cherry’s “direct opposition to the SNP’s stated policy on conversion therapy”, and referenced “a number of other actions and comments in recent months” that led to the call.
On Twitter, the group wrote: “It is clear by her actions and comments that not only does Ms Cherry oppose the party on a number of areas of policy, but she is content to undermine the party and the leadership in these areas.
"If the party’s code of conduct and standing orders are to have any meaning, they should be applied equally to all members, regardless of status, and we believe that no member should be above reproach.”
In January, Ms Sturgeon made a direct plea to young members of the SNP as concerns over the party’s tolerance for alleged transphobia led to scores of young activists leaving the party.
In it, the First Minister said transphobia should be treated with “zero tolerance” and was “not acceptable”.
The SNP has not responded to requests for comment.
Reacting, Ms Cherry reiterated her defence of her comments around conversion therapy.
She said: “The Scottish National Party has a long history of intellectual rigour and open debate and I trust that will continue, notwithstanding the personalised attacks and misrepresentation by some in my party.
"Sadly, calm and rational discussion has been missing from this area of public policy for too long.
“Last night I attended a debate hosted by the Middle Temple where representatives of Stonewall, gender critical feminists and the LGB Alliance held a respectful and engaging debate on the problems raised by draft proposals on banning conversion therapy.
"As a lesbian I welcome the ban on conversion therapy as it is conventionally understood.
"However, I share the concerns of many that the inclusion of the concept of ‘gender identity’ in the UK Government Bill risks threatening professionals working with children and vulnerable people who are having issues with their gender if they seek to explore with them the reasons for their distress.”