Allen had originally been set to launch a restaurant in Manchester with Select Property Group this year, but announced he had parted ways with the project in December.
The restaurant will be renamed Tim Allen's Flitch of Bacon when he takes the reins in February, serving seasonal, British cuisine 'with a modern edge'.
“The Flitch of Bacon is a special venue and, with my wife Magali, we would like the food, service and hospitality to match," says Allen.
"Ultimately we wanted the opportunity to run our own business."
Clifford opened The Flitch of Bacon in 2015 and it is recommended in the Michelin Guide, but does not currently hold a star or Bib Gourmand.
“Tim worked with me at Midsummer House so having [him] join me once again, this time in his own right as chef partner, is a huge deal for The Flitch and one that will see the already high standards of the restaurant improve even more," says Clifford.
“Due to the intense commitments of running a two Michelin star restaurant in Cambridge, there’s no one I’d trust The Flitch with more than Tim in his capacity as chef and partner."
Allen won a Michelin star at the Wild Rabbit in Kingham in 2016, but left the pub last August.
He previously worked as head chef at D&D London’s Launceston Place, with the restaurant winning four-AA-rosettes and a Michelin star under his tenure, and cooked under Martin Burger at two-Michelin-starred Whatley Manor in the Cotswolds.
Clifford has held two Michelin stars at his Cambridge restaurant Midsummer House since 2005.