The 40-year-old former politician had denied embezzling £21,000 while Women For Independence treasurer between April 26, 2013, and November 30, 2015.
She also denied taking £4,661 between April 9, 2014, and August 2015 while treasurer, secretary and convener of the Glasgow Regional Association of the SNP.
But a jury at Glasgow Sheriff Court returned two guilty by majority verdicts following a six-week trial.
Sheriff Tom Hughes had told jurors to ignore the publicity the trial attracted and focus solely on the evidence presented by the prosecution and defence.
The jury had been told that in order to convict McGarry, they would have to be confident beyond reasonable doubt that the funds were misappropriated and used dishonestly.
McGarry, of Clarkston, East Renfrewshire, who represented Glasgow East between 2015 and 2017, spent several days giving evidence in her own defence.
Earlier evidence was heard from several witnesses, including current and former Scottish health secretaries Humza Yousaf and Jeane Freeman.