The Global Equality Fund, administered by the US state department, has given the organisation more than £500,000 during the past three years, before Mr Trump ordered a halt to the spending.
But Lucy Hunter Blackburn, a former senior Scottish government civil servant who was previously responsible for funding external organisations, said it appeared Stonewall Scotland had become a “shell company” and that it was unclear why funding was continuing.
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“Stonewall’s dedicated Scottish staffing appears to have dwindled to nothing,” Ms Hunter Blackburn told The Sunday Times. “Stonewall Scotland’s social media accounts have been dormant for months and the programme Scottish Government funding is meant to support appears at first sight to have had little Scottish activity for some time.”
The charity says it has merged all individual roles into a more senior head of nations role and still has a senior staff member overseeing work across Scotland, Wales and Northern Ireland.
The Scottish Government has handed over more than £400,000 to Stonewall since 2022, under a funding arrangement to run a programme aimed at “advancing LGBTQ+ equality in Scotland”.
Under a binding contractual agreement, the cash was earmarked to help fund staffing costs for the equivalent of 3.75 full-time jobs.
However, despite Stonewall advertising for a Scotland director more than a year ago, the post appears not to have been filled permanently and it is not clear that it any longer has any dedicated staff north of the border, The Sunday Times reported.
The Scottish Government has agreed to continue funding Stonewall into the next calendar year. Funding from the Scottish, as well as the Welsh governments, has become increasingly vital to Stonewall as other governments, both in the UK and overseas, cut back on grants.
According to its most recent accounts, the devolved administrations now account for about half of Stonewall’s overall government funding, excluding lottery cash.
The Scottish Government’s funding for Stonewall comes on top of its significant backing for other LGBT groups, including almost £500,000 for LGBT Youth Scotland and £600,000 for the Equality Network.
The organisations have been vocal in support of SNP’s equality policies, such as Nicola Sturgeon’s gender recognition reform GRR) bill which aimed to make it easier for transgender people to change their legal gender by obtaining a gender recognition certificate.
It allowed trans people to self declare their gender and not have to obtain a medical diagnosis of gender dysphoria.
But the GRR legislation was blocked from becoming law by the previous UK Conservative government. The GRR bill was also opposed by the Conservatives in Holyrood, the only part to do so.
Tess White, the Scottish Conservative’s equalities spokeswoman, accused the Scottish Government of wasting money by funding Stonewall.
“Scots will ask serious questions as to why the SNP is squandering so much taxpayers’ money still funding this organisation that has been mired in controversy,” she said.
“With the SNP still wedded to their gender policy, many will wonder if this money is being continued to shore up Stonewall’s support for this agenda.
“Ministers must finally do the right thing and ditch their gender obsession as well as stopping giving a six-figure sum to an organisation that doesn’t appear to be active in Scotland.”
A spokesman for the Scottish Government said: “We are committed to supporting LGBTQI+ people, including through funding for Stonewall to advance equality for this group.
“This is particularly important at a time when we are seeing a rise in attacks against the LGBTQI+ community.”
A Stonewall Scotland spokesman said: “As we see an increasing roll-back of hard-won rights globally, the work to advocate for LGBTQ+ equality has never been more important.
Stonewall remains committed to improving LGBTQ+ rights across the four nations, including Scotland.
“Stonewall has worked in partnership with other LGBTQ+ organisations and partners in Scotland for 25 years and we continue to do so.
“We support a significant number of workplaces in Scotland on their inclusion journey and have a proud record of supporting the Scottish government on their policy and legislative ambitions. We hope that the introduction of a UK-wide fully inclusive conversion practices bill for all lesbian, gay, bi and trans people will be forthcoming in the next month.”