After undergoing a hip operation this year, the former UTV journalist said he was quitting the show to concentrate on other television projects.
For more than a decade Holmes anchored the flagship breakfast programme as well as juggling gameshow roles, regularly hosting the National Lottery and a weekly Friday morning slot on ITV's This Morning with wife Ruth Langsford.
He was often dubbed the busiest man on television.
And managing several jobs sometimes took its toll. In 2010 the avid Manchester United fan got stuck in traffic as he rushed from Sky to ITV forcing Richard Madeley - who was set to appear as a guest - to turn back the clock and fill in alongside Langsford until Holmes arrived.
And the presenter missed Sunrise completely last year after becoming stranded by fog which grounded his London-bound flight.
The Northern Irishman signed a five-year contract at Sky in 2013 but announced his intention to leave last month via a post on his Facebook page. He called anchoring his own breakfast show "the stuff of boyhood dreams" but said that it is time for him to step down due to "having so much to do but little time to do it".
He said: "Anchoring my own breakfast show for 11 years has been for me the stuff of boyhood dreams. It was the job I hoped to do as a young Belfast lad - and because of Sky News I got there.
"Forty-five years plus on I have other dreams, and to achieve them I realise that unfortunately I need to step away from the daily studio commitment for a while.
"There is an addiction to a live breaking news studio environment... it is a habit I have to suppress."
His approach was revealed as "very much 'be yourself'" by former co-host Charlotte Hawkins, who credited Holmes with developing her career before she made the move to Good Morning Britain two years ago.
However, it has not all been plain sailing for Holmes. Earlier this year he had to apologise after being accused of comparing an attack on the Manchester United team bus by West Ham supporters to the 1989 Hillsborough disaster, which led to deaths of 96 Liverpool fans.
In stepping down, Eamonn will end his run as the longest serving breakfast news anchorman in Britain.
He will continue to host ITV's This Morning on a Friday along with Ruth as well as other television projects.
There has been speculation that the couple may want to spend more time together away from the studio after years of gruelling schedules.