McGarry, who represented Glasgow East but did not seek re-election in 2016, appeared in private at Glasgow Sheriff Court today.
She made no plea and was bailed pending a further court appearance.
McGarry was elected as an SNP member in 2015, but resigned as the party whip following the emergence of fraud allegations, which she denied at the time.
She appeared in court under her married name Natalie Meikle.
The former MP was charged with three counts of embezzlement, two charges under the Scottish Independence Referendum Act 2013 and one charge under the Regulation of Investigatory Powers Act 2000.
The charges under the referendum act relate to “knowingly or recklessly making a false declaration” regarding referendum expenses and allegedly failing to comply with requirements regarding referendum expenses.
The Regulation of Investigatory Powers Act charge involves allegedly knowingly failing to comply with a notice regarding disclosure of protected information.
McGarry was elected as an SNP member in 2015, but resigned the party whip following the emergence of fraud allegations which she denied at the time, continuing in parliament as an independent.
She was one of the 56 SNP MPs elected in the 2015 poll.
McGarry announced in April last year she would not be seeking re-election.
The ex-Glasgow East MP said at the time it had been a “huge honour and a privilege” to have represented her constituents in the House of Commons for the past two years.