He will step down “sometime in May”, a spokeswoman for ScotRail said.
The news came as it was also confirmed that senior Network Rail executive Phil Verster would lead a new ScotRail-Network Rail closer-working “alliance”, and start work shortly.
The ScotRail franchise is a key part of the Scottish economy - it is the Scottish Government’s biggest contract, worth some £2.5 billion, and employs some 5,000 people.
Abellio surprised the rail industry by announcing last Tuesday that Mr Montgomery would keep his job after it takes over the train operator next Wednesday.
This was despite current ScotRail operator FirstGroup losing the contest to run the next ten-year franchise to Abellio.
In last week’s statement, Abellio said: “The new team will continue to be led by Steve Montgomery as managing director.”
The latest development means staff have gone from not knowing who will lead them until two weeks before the start of the franchise, to being told there would be no change at the top, to now hearing that this will change in little more than a month.
It had been thought a management shake-up would follow when the alliance between ScotRail and Network Rail was formed.
However, that has now started with Mr Verster moving from his current job as route managing director of the track firm’s London and North East region, which includes the east coast main line.
He was previously deputy chief executive of Irish Rail and engineering director for South Trains in England.
Mr Verster said: “The alliance between Abellio ScotRail and Network Rail gives us a unique opportunity to establish new ways of working and to improve what we deliver for the travelling public and our communities.
“This is a very exciting time for the railway in Scotland and my approach is all about listening to our communities and to focus on what is important to our customers.”
A Network Rail spokesman said: “Over the coming weeks, Phil will work closely with Abellio’s mobilisation and transition team, the ScotRail leadership team and Network Rail to plan and organise the alliance transition arrangements, as well as facilitating an orderly and effective hand over from Steve Montgomery who has agreed to lead the new ScotRail franchise during the initial period of operations.
“Steve’s leadership will ensure continuity in service quality for customers.
“We would like to take this opportunity to recognise Steve’s tremendous contribution to ScotRail and wish him every success in the future.”
Network Rail managing director of network operations Phil Hufton said: “Phil brings a wealth of valuable experience to what will be one of the highest-profile roles in the industry.
“He has achieved great results during his time on the east coast mainline and I look forward to him bringing that same positive approach to leading the railway in Scotland.”
Abellio UK managing director Dominic Booth said: “We are confident that Phil brings the requisite skills and experience to drive transformational change in order to deliver against our ambitious plans for the improvement of rail travel in Scotland.”
Transport Minister Derek Mackay said: “I welcome this next step in the development of the Deep Alliance between ScotRail and Network Rail and the positive impact that closer industry working will have on performance and the passenger experience.”
SCOTSMAN TABLET AND MOBILE APPS