The 33-year-old, who started his career at Aberdeen and had a brief spell on loan at Kilmarnock before leaving Scottish football in 2011, is alleged to have placed 52 bets on football matches between March 2017 and February this year.
He has been given until Tuesday, August 30 to respond to the misconduct charge.
The period of Maguire’s alleged offending includes time spent at former clubs Oxford, Bury and Sunderland.
“Chris Maguire has been charged with misconduct in relation to an alleged breach of the FA’s betting rules,” read an FA statement.
“It is alleged that the Lincoln City FC forward breached FA rule E8 by placing 52 bets on football matches between 17 March 2017 and 12 February 2022.”
Maguire, who was capped twice by Scotland in 2011 in the Nations Cup, joined the Imps last summer and has made three appearances in all competitions this season.
A statement from the Sky Bet League One club read: “Chris has been suspended by Lincoln City without prejudice until further notice.”