The council is taking extra measures as work continues between the Clapham Road and Paula Radcliffe Way roundabouts.
Queues have been horrific so the council is keeping both northbound lanes out of town open during peak periods to create more space for traffic.
However, during off-peak periods they will be closed to allow lorries into the site.
The bulk of the works are also being moved to overnight.
The widening of Clapham Road between the two roundabouts is already complete, along with the dedicated left hand turn lane from Clapham Road into Manton Lane.
And work has begun on the central reservation between the Clapham Road and Paula Radcliffe Way roundabouts to introduce a permanent right hand turn into Sainsbury’s.
This means people won’t need to use the Clapham Road/Manton Lane roundabout to U-turn and so reduce traffic on this busy roundabout.
Cllr Charles Royden, portfolio holder for transport and highways, said: “We are constantly reviewing and trying to find ways to reduce the disruption as we work to deliver these improvements works on a well-known congestion hotspot in Bedford.
“Hopefully motorists and other roads users will see some improvement with overnight works enabling us to open more of the road during busy times, and manual control of the lights so we can help traffic to move as well as possible.
“We apologise for the disruption being caused and thank you all for your patience as we complete this project.”