Watson will move to Scotland to take up the job at the newspaper and magazine distribution firm in September.
Watson joined MGN as general manager in 2003 and was appointed managing director of the nationals division with responsibility for the UK and Scottish national titles in May 2004.
He joined Trinity Mirror from 'Who Wants to Be a Millionaire?' firm Celador International, where he was managing director.
Prior to that, he came to prominence in his role at News International where he was marketing director for News Group, which publishes The Sun and News of the World. He also headed up News International's short-lived Currant Bun ISP, which later became The Bun.
When he joined Trinity Mirror, he was one of chief executive Sly Bailey's first senior appointments.
"I've loved every thrilling moment in this wonderful business working alongside many of the most talented people in newspapers. I'm really grateful to Sly for giving me the opportunity to oversee some of the UK's best-loved titles and in doing so to post a cracking set of results," Watson said.
Watson, whose family live in Scotland, said the move was prompted by family life.
"Ellis comes from Planet Tabloid and we are all going to miss his flamboyance, his dreadful dress sense and of course his unswerving modesty," Bailey said.
Based in Edinburgh, Ellis will be joining one of Scotland's largest companies, which was also one of the UK's biggest newsagents before selling off most of its business to WH Smiths.
John Menzies chairman William Thomson said: "We are delighted to appoint Ellis, who is well respected in the industry, to this important position for John Menzies. He brings a breadth of industry experience to Menzies Distribution and a wealth of skills and talents to our senior leadership team."
Ellis added: "John Menzies has a strong management team and a robust position in its sector. I am looking forward to the opportunity to build on its solid base."
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