Anglia Railways and First Great Eastern have lost their franchises running intercity, commuter and local train services.
The Strategic Rail Authority (SRA) has chosen rail and bus operator National Express over Anglia as the preferred bidder to run services between London, Cambridge and Norwich.
First Group, which owns First Great Eastern and Anglia Railways, had been confident of gaining the newly-expanded franchise to operate trains across the region.
But on Monday the SRA said National Express was to run the new Greater Anglia Franchise, which combines services currently run by Anglia, First Great Eastern and the West Anglia part of West Anglia Great Northern.
Sunderland-based Arriva bus and rail firm has also lost out in the bidding.
The new franchise will run for seven years, with an option to extend it to ten years.
The SRA said the new franchise would bring better passenger information, security and station improvements as well as improved punctuality.
But a spokesman confirmed the deal would not include new trains or replace old carriages and locomotives on the London to Norwich intercity route.
Instead, National Express is likely to replace the old slam-door carriages with refurbished carriages, possibly from Virgin Railways.
The spokesman said: "We think this deal is extremely good value for taxpayers and passengers."
But First Group said it was "extremely" disappointed not to be awarded the franchise.
Derek Monnery of the Manningtree Rail Users Association in Essex said they were also disappointed as First Group had won several awards for being a good operator.
The Liberal Democrat MP for Colchester, Bob Russell, described it as a dark day for commuters as there was little chance of any change.
"This is just a bad day for the rail travelling public of Essex."