Mr Matheson was suspended from his job as head of Hermitage Academy in Helensburgh last June amid allegations of financial irregularities. It was claimed that he had been charging an ice-cream van owner pound;10 a day to sell sweets, snacks and burgers inside the playground.
Auditors from Argyll and Bute Council looked into the accusations and Mr Matheson was removed from his post. Police were called in.
In a remarkable set of circumstances, Mr Matheson last week was handed an early retirement package by the council on the same day he was appearing in private at Dumbarton sheriff court.
A Crown Office spokesman said: "He appeared on petition in private on January 31 charged with embezzlement and made no plea or declaration. The case was carried forward and Mr Matheson was bailed."
It is likely Mr Matheson will face trial at Dumbarton sheriff court after further investigations.
Mr Matheson has been a prominent member of the HAS and was a key negotiator during the post-McCrone talks in 2000 on teachers' pay and conditions. He has recently been a member of the General Teaching Council for Scotland and occasionally chaired its disciplinary committee.