Pubco Greene King said internal refurbishments would maintain the building and preserve its historic elements while improving customers’ eating and drinking experience.
The Eagle Inn was the spot where Cambridge scientists Francis Crick and James Watson declared their discovery of the double helix structure of DNA in 1953.
With the University of Cambridge's Cavendish Laboratory a short walk away, the pub was a local haunt for researchers.
Crick and Watson received the Nobel Prize in Physiology or Medicine, alongside Maurice Wilkins, in 1962.
A section of the ceiling also features signatures from RAF pilots who drank at the pub when they were positioned in the city in World War II and used cigarette lighters to mark the bar.
The pub was listed in 1950 for its historic significance as a traditional 16th century coaching inn, and hosts a blue plaque celebrating the DNA discovery.
Cambridge City Council approved an application from Greene King to carry out refurbishments and repairs.
Greene King said the pub would be closed for a short while but the work would not take place until early next year.
It pledged that improvement work would not be detrimental to the historic fabric of the pub and would allow it “to offer customers an improved experience”.
Some sections of flooring and roofing will be refurbished in the six-figure investment and a bulkhead for new lights added to the scorched ceiling.
Improvements are set to include new counter-tops and alterations to joinery, in addition to a revamp of the pub’s basement toilets.
A Greene King spokesperson said: “As responsible custodians of this historic pub, we are pleased to learn the local authority has granted permission for us to undertake some minor internal refurbishments to maintain the building and keep it preserved for generations to come.
“The investment will be made in updating the kitchen operations to improve the speed of service, refurbishing the toilets and some minor updates to the décor of the dining and bar area.
“We’ve taken careful consideration with every decision to ensure the updates enhance the pub’s unique style and features, and will not be detrimental to the conservation area.”