His announcement came just hours after Steve King's appointment as manager at the Moss Rose.
Former Lewes boss King has been unveiled as the man charged with guiding the Silkmen back to League Two at the first attempt.
But ex-Macc player Scott has opted not to remain in the boardroom as the Cheshire club campaign in the Blue Square Bet Premier, telling the club's official website: "It's with a heavy heart that I will be stepping down.
"I've enjoyed my time immensely whilst on the board for six years.
"Relegation from the Football League was a bitter pill to swallow for everybody involved with the football club and, believe me, it's still hurting now."
Chairman Mike Rance added: "I totally understand Andy's decision to stand down. We're entering a new era at the Moss Rose and it's a good time for someone new to take the club forward."