The pop-up mall – which houses a mix of retail and restaurant operators in shipping containers – will see its upper floor transformed in to a new street food area.
Work will begin in May to close off part of the top deck and build a clear ceiling over the central dining and events space.
The construction will also create room for new food and drink outlets to join the development.
Boxpark said the changes would keep visitors protected from the elements and encourage people to use the site all year round.
Boxpark Shoreditch first opened in 2011 and features restaurants such as Voodoo Rays pizzeria and Bukowski Grill.
Soft Serve Society, The Athenian, Duck Truck and Arni's Grill all joined the development last year.
A second Boxpark, which features only food and drink outlets, opened in Croydon in 2016.