The London restaurant, which opened in 2002 and ran its famous Pay What You Think It's Worth promotion, has been sold off to another operator and will close on 25 September.
Ilic plans to use the capital from the restaurant's sale to invest in his healthy fast food brand Foodilic, which he hopes to grow to 30 sites in London by 2019.
A statement from Little Bay thanked customers for their 'loyal support' of the 'little restaurant' over the last 14 years.
"It is thanks to you that Little Bay has become such a well-known eatery across London and around the world," it said.
Little Bay restaurants remain in London's Kilburn and Croydon. The brand's Brighton restaurant closed in February while its Battersea restaurant remains 'temporarily closed'
Following the success of two Foodilic branches in Brighton, the grab-and-go concept with an emphasis on 'nutritious and delicious food' spread to London's King's Cross in 2014.