Irons helped guide the Second Division side away from relegation and then to a fifth-placed finish last season.
Stenhousemuir have issued a statement via their website, it read: “It is with great sadness the club has to announce the resignation of David Irons as Manager of Stenhousemuir FC. Davie has had to stand down due to personal issues.
“The club would like to thank Davie for the tireless work he did at the club, leaving us in a far stronger position than when he initially took over.
“The club would like to wish David and his family all the best in the future and I’m sure our supporters would echo the clubs thanks.”
After the resignation of Irons, a former charge of his, William Lyle hit out at his former manager via twitter.
Lyle commented: “I’m not bitter but thanks Davie Irons for ending my Stenny career then chucking 2 months later was always going to happen #joker”
The 28-year-old signed for Stenhousemuir in June 2007, making 169 appearances and scoring seven goals.