The locations include Chestnut Hill on Germantown Avenue in Philadelphia, Main Street in Newark, Delaware, and Town Center Boulevard in Voorhees, New Jersey.
The company says its 16 remaining restaurants across the region will remain open.
In a statement, Iron Hill said the closures are part of its ongoing efforts to adapt to a changing business landscape while focusing on long-term growth and success.
"While we are closing a few locations, this is truly part of a larger growth story - we are evolving, strengthening our brand, and positioning Iron Hill for long-term success," said Mark Kirke, CEO of Iron Hill Brewery & Restaurant.