A revised timetable has started that will last until December.
Senior figures at ScotRail said the engineering work was being undertaken as part of a plan out to boost reliability and prepare for the arrival of new electric trains.
Some services will be replaced by buses and queuing systems will be in place at key stations.
This is because trains could be diverted, less frequent or cancelled.
Jacqueline Taggart from the ScotRail Alliance said: “We are going through a massive period of change on Scotland’s railway.
“The work that we are carrying out over the next few months will bring about a revolution in rail, with more and better trains, more services and more seats than ever before.
“However, while we transform the railway, there is inevitably going to be some impact on people’s services.
“We are doing everything we can to minimise this, and to keep people moving.”