Under the agreement, KKR will pay £418m over 10 years to plug the deficit in the scheme, and allocate a further £600m as a potential safety net.
The Alliance Boots pension scheme has 66,000 members, including 16,000 employees who are still making contributions.
“We are pleased to have reached a satisfactory agreement on the future funding and security of the Boots pension scheme,” said John Watson, chairman of the pension trustees.
Retail union Usdaw said the agreement was good news for its members.
“Our members who are paying their pension contributions told us loud and clear that they were worried about the future of the scheme, said Usdaw general secretary John Hannett. “This agreement appears to address those concerns and put their minds at rest that they can retire on a decent pension.”
The takeover is now set to be completed in July, and will be the first time a FTSE 100 firm will be de-listed and taken private.