“I don’t want to do that,” Mr Flynn told BBC Scotland’s Sunday Show. “I live in Aberdeen. This is where my life is. I’m very fortunate to represent the people here.”
The party boss also defended his surprise bid to represent the city at both Holyrood and Westminster, saying it would save taxpayers and other political parties hundreds of thousands of pounds.
He also declined to rule out a bid for the SNP leadership, though said he thought there would not be a contest for a “long, long time.”
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The deadline for applications to be considered for selection as an SNP candidate for the Holyrood 2026 election closed on Monday.
Mr Flynn revealed on Tuesday that he is seeking to be selected as the candidate for Aberdeen South and North Kincardine, currently represented by Ms Nicoll.
His intention, if elected, is to stay on as the MP for Aberdeen South.
In 2020, the party’s ruling NEC made it harder for politicians to hold dual mandates.
They required any MP picked to stand for Holyrood to quit their Westminster seat and trigger a by-election.
At the time, it was widely seen as a ploy to stop Joanna Cherry heading to the Scottish Parliament.
Asked about the decision, Mr Flynn told the programme he did not know why the NEC had taken that decision: “I can only speculate as to the reasons why that took place. I think some are perhaps speculating with a more accurate degree of detail than others in that regard, but that’s for those people on the NEC to outline why they did that.
‘The party’s position for decades beforehand was to allow people to represent their constituents in Edinburgh and in Westminster. I believe I can do that.”
Mr Flynn said he would not take two salaries if elected to Holyrood while still an MP.
He also said his serving in both parliaments “would save the public purse a significant amount of money by not causing a by-election.”
“Tens of thousands, if not hundreds of thousands of pounds. And of course, in doing so, I would save all the political parties the necessity of spending up to £100,000 on a by-election campaign.”
Mr Flynn said press reports that he had asked Ms Nicoll to stand aside the night before details of his bid first appeared in the Press and Journal were a “lie”.
“I did call Audrey before, we had a fairly cordial conversation, albeit brief. Myself and Audrey speak relatively frequently, as I’m sure you can imagine.
“I made clear to her my intentions. Audrey, of course, suggested that some had been thinking that I may seek candidacy in Dundee, which I assume would be a much bigger story.
“I don’t want to do that. I live in Aberdeen. This is where my life is. I am very fortunate to represent the people here.
“She told me that she wasn’t overly surprised at the decision that I was taking, that I was obviously seeking to progress my activities in politics and that was, ultimately, the end of the conversation.
“I had hoped it had happened sooner. There’s obviously been significant goings on in Aberdeen locally with regards to politics, and I thought it was best to leave Audrey to deal with some of that.”
Ms Nicoll’s husband Alex recently quit the SNP group on Aberdeen City Council in protest at the party’s position on city centre bus gates.
Mr Flynn said he was also “dealing with other things” in his own personal life which made it difficult to speak to his colleague sooner.
“None of this is particularly edifying for anyone,” he Flynn added. “I don’t want to be doing this. I don’t want to be having these discussions on television, trying to defend myself over lies and fabrications that are in newspapers this morning.
“But that’s the reality of politics. Sometimes it’s not pleasant.
“And you know, I’m not going to shy away. I’m not going to be hounded out from standing for what I believe in, which is to represent the people of Aberdeen South.”
A source close to Ms Nicoll told the BBC that while Mr Flynn had not directly asked her to stand down, she felt as if there had been an “underlying inference” that she should not contest the selection.
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Asked if he had told John Swinney about his decision, Mr Flynn said he “had conversations with people right across the party” including “key local activists.”
He added that the First Minister was, “of course aware of what my intentions are”
“The people who needed to know what my intentions were were aware of what my intentions were, because I want to act in the best interests of the party.
“Let me be very clear, if the leadership of the party through the National Executive Committee determined that they don’t want me on the pitch at the Holyrood elections, I will continue to do my job of campaigning heart and soul for the Scottish National Party from the bench or from the stands, because I believe that we need to win the Holyrood elections for the best interest of the SNP and the best interests of the people in Scotland.”
Asked if he fancied a “crack at the leadership,” Mr Flynn replied: “So I’m ambitious. I’m seriously ambitious for Aberdeen and for Scotland.”
When the host interjected to ask if he was ambitious for himself, Mr Flynn replied: “I don’t think that’s called for.”
“I don’t believe that there’s going to be a leadership contest in the Scottish National Party for a long, long time, because John Swinney is going to win the Scottish Parliament elections in 2026. He’s going to continue as First Minister.
“And should there be a future leadership election, it will be in the dim and distant future.”