The 29-year-old striker is accused of placing seven bets on six Ayr matches, and an additional 150 bets on other fixtures.
However, the SFA have stressed there is no evidence to suggest Moffat has been involved in match-fixing or influencing results.
A hearing for the case has been scheduled for January 16, while Moffat has until December 24 to respond to the charges levied against him.
Moffat was served a notice of complaint by the SFA, with the compliance officer making reference to two breaches of disciplinary rule 33.
The rule reads: "No club, official, team official or other member of team staff, player, match official or other person under the jurisdiction of the Scottish FA shall bet in any way on a football match (except authorised and registered football pools)."
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