The 33-year-old is alleged to have placed a total of 52 bets on matches between March 2017 and February 2022.
The FA said that this breached Rule E8 on betting, which bans any player, match official and coaches from level eight in the English football pyramid and upwards from placing bets on games anywhere in the world.
Individuals found to have breached this rule face a fine, suspension or ban from the game.
Lincoln City, which plays in League One, also confirmed that Maguire had been suspended from the club “without prejudice” until further notice.
Scottish forward Maguire signed for Lincoln City in the summer of 2017 and scored five goals in his first season with the club, including a hat-trick against former team Sunderland.
Maguire has been capped twice by Scotland and also played for Derby County, Sheffield Wednesday, Oxford United and Rotherham United.