Beattie, appointed by the League Two club in May, did not have a UEFA B licence when he took the job and has subsequently failed to gain the qualification.
Football League rules require managers of clubs in League One and League Two to have a UEFA B licence and be working towards a UEFA A licence within three years of their appointment.
The organisation reminded Accrington of their responsibilities after the departure of former boss Leam Richardson in April and again when Beattie was appointed.
And a result of the club not meeting these requirements, the Football League imposed the fine - £15,000 of which is suspended subject to Beattie achieving the necessary qualification by May 1 this year.
A statement on the Football League website read: "A Football Disciplinary Commission (FDC) has fined Accrington Stanley £20,000 for breaching Football League Regulations regarding manager coaching qualifications.
"The three-man commission, appointed under the Regulations of The Football League, found that Accrington Stanley, in appointing James Beattie as its first team manager, had breached Regulation 40.
"As of the date of the FDC hearing (Jan 2014), James Beattie had still not attended a relevant course or been able to confirm a place on a future course."
Accrington can appeal the FDC's decision within 14 days.
