The government says it wants to give people in northern England "more powers over their railways" as it starts running services previously operated by Arriva Rail North.
The takeover was announced in January following widespread commuter chaos.
Greater Manchester mayor Andy Burnham will be among a panel of northern political leaders who will advise the government's operation.
Transport Secretary Grant Shapps said there would be "no quick fix".
Passengers have experienced regular delays and cancellations since a timetable change in May 2018. They also faced strikes and an ageing fleet of trains.
German firm Arriva, which had been due to run Northern services until 2025, previously said problems had been largely due to "external factors" such as infrastructure.
A Department for Transport spokeswoman said tackling overcrowding would be a priority, with "new technology being trialled to identify crowding pinch points".
The government also said:
- Work will continue to extend platforms at 30 stations to allow for longer trains.
- A major deep-cleaning program has started on carriages.
- More electric trains will be introduced across the Northern network next year.
Transport Secretary Grant Shapps said: "This is a new era for rail in the North, but there will be no quick fix for the network as we build solutions for the future.
"Our aim is to give the North of England more powers over their railways, restoring the confidence of passengers and delivering a network they can truly rely on."
In October, Mr Shapps revealed he had requested a proposal from Northern to outline its improvement plans after "unacceptable" delays.
The Department for Transport then considered whether to hand a new, short-term contract to Arriva, or to nationalise services by putting the government-controlled Operator of Last Resort (OLR) in charge.
OLR already manages the London North Eastern Railway (LNER) franchise after railway services on the East Coast Main Line were brought back under government control in May 2018.
Northern services have transferred from Arriva Rail North to Northern Trains Limited - a newly-formed subsidiary of OLR.
A campaign for the operation of Northern services to remain in public ownership will be launched by rail union RMT, passenger groups and politicians on Monday, with demonstrations at northern stations.
Kate Anstee, from the Northern Resist passenger group, said: "We welcome Northern being finally taken into public ownership, but we hope the Government doesn't sell it off at the first possible opportunity."
The Northern branding on the trains will remain and staff will continue in their jobs.