The incident at First Ministers Questions was later dismissed as a "bizarre intervention" by a spokesman for Nicola Sturgeon.
The weekly session was briefly halted by Presiding Officer Ken Macintosh while two men were ejected from the Holyrood public gallery.
The protest appeared to target the SNP's John Mason who apologised three years after suggesting some people saw IRA terrorists as "freedom fighters." Mr Mason was also at the centre of a furore last week when he suggested that he would not represent pro-UK constituents.
One of the protesters was heard to shout: “Why do so many in your party support the IRA? They’re not supporting unionists in society.”
When other people in the chamber reacted with baffled cries of “What?”, the man continued:
“How many support the IRA in your party, Nicola? John Mason called them Irish freedom fighters, did he. He doesn’t support unionists. SNP IRA!”.
Mr Mason later left the chamber flanked by fellow SNP MSPs Christine Grahame and Roseanna Cunningham and refused to take questions from the media.
Mr Cunningham, the environment secretary, advised him: “Don’t engage”.