The former England international took the reins at the club in May last year and guided the team to 15th in League Two in his sole full season in charge.
Accrington have endured a troubled start to the 2014-15 campaign, winning just one of their opening six league outings.
That victory arrived on Saturday - a 3-2 home success over Tranmere Rovers - but the club announced on Friday that Beattie had departed.
"Accrington Stanley Football Club and James Beattie have decided to terminate their contract by mutual consent with immediate effect," a statement on Stanley's official website read.
"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."
Beattie expressed regret that his first stint in management had ended in such fashion.
"It is with a hugely heavy heart that I decided to end this journey," he said. "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 per cent.
"I thank them from the bottom of my heart for granting me the opportunity and privilege to be part of your unique club."
Assistant manager Paul Stephenson will take charge of Stanley's home clash with AFC Wimbledon on Saturday.
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