The blue and orange toll plazas, which span eight lanes, are being demolished to allow a new, more efficient road layout to be created.
The road works are due to be completed in spring 2022.
It is the second phase of the Tyne Pass project which saw open road tolling introduced at the tunnels on November 8, where customers drive straight through and either pre-pay or pay after their journey.
The northbound toll plazas at Wallsend will be the first to be dismantled.
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Soon, customers travelling north will be filtered into lane numbers 7 and 8, as part of two continuous lanes heading through the tunnels.
To help ease congestion, some of the structure has already been removed to create wider lanes to pass through.
The northbound tunnel will be closed on Friday, December 3, at 10pm until Monday, December 6, at 5am.
During this time, the southbound tunnel will be operating as bi-directional.
Shaun Simmons, customer operations manager at TT2, who operate the tunnels on behalf of the North East Combined Authority, said: “The works to dismantle the toll plazas will be completed as quickly as possible and we are managing the road to ensure minimal disruption to drivers.
“Any changes, like these, will naturally take a little getting used to, but the plaza removal will, when complete, make journeys faster and smoother.
“We will continue to monitor the traffic flow and keep drivers informed of the progress.”
Drivers no longer have to stop at toll plazas, driving straight through and either pre-pay or pay by midnight the day after their journey.
Drivers can pay online at tt2.co.uk, over an automated phone line on 01915740030 or at PayPoint retailers. They can also set up a Pre-paid account with auto top-up and save 10 per cent on every journey.
Around 75 per cent of customers now use a pre-paid account to pay for their journeys.
Pre-paying also makes each journey 10 per cent cheaper and is free to set up and use.
To find out more about Tyne Pass, visit www.tynepass.co.uk