The former England striker has had his contract terminated following the club's start to the League Two campaign, which has resulted in four defeats, one draw and just one victory.
Beattie told the club's official website: "It is with a hugely heavy heart that I decided to end this journey. I can never fully repay the faith and backing I got from the players, my staff and of course the fans who always gave me 100%.
"I thank them from the bottom of my heart for granting me the opportunity and privilege to be part of your unique club."
The 36-year-old took on a player-coach role with Accrington back in November 2012 before being appointed as full-time manager in May the following year.
A statement from the club said: "Everyone at Accrington Stanley would like to thank James Beattie for all his efforts during his tenure at the club and wish him and his family all the best for the future."
Assistant manager Paul Stephenson will take temporary charge of the first team for tomorrow's match against AFC Wimbledon on home turf.