[5] As of January 2025, it has restaurants in Massachusetts: Beacon Hill and South End, Boston, Brookline, and Lexington;[6] and Beverly Hills, California,[7] A United States Department of Labor investigation of the company's pay practices from April 2007 through April 2009 revealed that Upper Crust's hourly workers were paid straight time even after they exceeded 40 hours in a week.

On December 20, 2010 a former operations manager at Upper Crust filed a lawsuit that accuses the Boston pizza chain of retaliating against him after he reported the company to the US Department of Labor for allegedly violating wage and hour laws.

In 2012, Upper Crust co-owners Joshua Huggard and Brendan Higgins sued Tobins, alleging that he had used more than $750,000 in company money for personal expenses such as the purchase of a small airplane.

[15] The location in Harvard Square was subsequently purchased by attorney Shannon Liss-Riordan, who had represented the chain's employees in a lawsuit, to be re-opened as a partly employee-owned pizzeria, the Just Crust, which closed in winter 2018.

[17] As of April 2013, Tobins or UC Acquisitions controlled the Upper Crust name and the locations in Beacon Hill, Brookline, Lexington, South End, Watertown, and Wellesley.

[17] Jordan Tobins later settled all legal matters related to his involvement with Upper Crust, including employees' back wages and all tax liabilities with Massachusetts.