Les Gray will take over from MacDonald as chairman of the First Division side.
In a statement on the official Accies website, MacDonald confirmed his departure, he said: “As you will be aware Allan McGonigal and Allan Maitland were appointed Directors of the Club last month. This strengthening of the Board was essential as I am now passing the Chairmanship to Les Gray and resigning as a Director with immediate effect.
“We are at a time in the season when decisions must be taken for the next and it is essential that the new Board have the opportunity to do so.
“I am delighted for Les who has been instrumental in creating and developing our Youth Academy and has always given me unstinting support.”
MacDonald added: “When taking control at Accies nine years ago my only stated objective was to leave the Club and the stadium in a healthier condition than I found it. With the help of many people this, I believe, has been achieved, and I would like to thank them all for their efforts.
“I must make special mention of Billy Reid for his achievements in developing players and giving the Club our most successful era of league performances, just a pity we couldn’t have stayed top of the Premier League.”
Accies currently sit in fifth spot 24 points behind First Division champions Ross County.