Kate Forbes has vowed to "serve all communities" in Scotland after the Scottish Greens claimed LGBTQ people were "afraid" because of her return to frontline politics.
The party is livid at John Swinney's decision to make the Skye, Lochaber and Badenoch MSP his deputy.
There has also been criticism from the SNP's LGBTQ wing, Out For Indy.
They say they "will be seeking urgent clarification from the FM and DFM that our progressive LGBTQ+ policies such as a ban on conversion practices will not be stalled or removed from the programme of government."
During First Minister’s Questions, Patrick Harvie asked if the new SNP leader's "vision for the future of Scotland" was to take the country "back to the repressive values of the 1950s?”
Later in the day, Ross Greer told MSPs that his party would vote against Ms Forbes’s appointment.
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However, a possible crisis for the government was averted when the Lib Dems abstained, and Alba's Ash Regan voted with the minority administration.
A number of opposition MSPs also did not take part in the vote.
In the end, Ms Forbes's appointment was approved by 63 to 57.
The Deputy First Minister, a member of the socially conservative Free Church of Scotland, came in for criticism during last year's SNP leadership contest over comments on gay marriage.
Though she was not a member of the Scottish Parliament when the legislation was passed in early 2014, she told an interviewer that she would have voted no if she had been.
In another interview, she said having children outside of marriage “would be wrong according to my faith.”
The comments led to a number of her backers quitting her campaign before it really started.
It also saw her criticised by Mr Swinney.
At the time, he said: “If Kate wants to set out those views, with which I profoundly disagree despite being a man of deep faith, then the party membership will make their judgment about those views and whether they think those views are appropriate for someone to hold if they are leader of the SNP and first minister.”
On Thursday, Mr Greer told MSPs: "There is not a credible argument for someone being an unsuitable First Minister, but a perfectly suitable deputy."
Mr Greer told MSPs: "My belief in the good news brought by Jesus Christ is something I share with Mr Swinney and Ms Forbes, and in that we share something far more important than party affiliation or political ideology.
“Faith is not the issue here. The issue is that I'm being asked to vote for someone who thinks there's something wrong with me."
He said many LGBTQ Scots were "afraid."
"I know that's not your intention, and it's certainly not the intention of Ms Forbes, but it's the reality."
Responding to the Scottish Green MSP’s comments, the First Minister said the country he leads today is a “modern, diverse, dynamic society” and that he wanted to keep it that way.
He said his whole government was committed to that.
"I want every single person in our society, to feel that they are at home and at peace in our society,” he added.
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Mr Swinney told Mr Greer: “I come to these conclusions from a very deep Christian faith. I believe that nothing can separate us from the love of God. That is the foundation of who I am. Nothing can separate us from the love of God and we are equal in the eyes of God."
"Every one of us.
"I hope those comments, which are more forthright about faith than I have ever uttered in my 45 years in politics, will perhaps illustrate to Parliament the magnitude of the seriousness with which I take the issues that Mr Greer puts to me.”
Speaking to journalists after First Minister’s Questions, Ms Forbes said: “I am here to support the First Minister and together we serve all communities in Scotland as we further and progress the rights of every community in Scotland, and I look forward to doing my part in achieving the Government’s aims in that regard.
“Not just that, but when I joined Government yesterday in a clear role to support the First Minister, I signed up to collective responsibility, so I stand by the Government’s decisions and agenda to improve and progress the rights of all of Scotland’s communities.”
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