A sixth Blackwater guard has brokered a deal with prosecutors, pleading guilty to killing one Iraqi and wounding another.
The company said Prince will focus his efforts on a private equity venture unrelated to the firm.
Prince, who founded Blackwater in 1997, said Joseph Yorio, a former US army officer, will become its new president, and Danielle Esposito, a current employee, will become the chief operating officer as part of what he called the company's "continued reorganisation and self-improvement".
The company changed its name to "Xe" last month, shortly after Iraqi officials revoked the company's licence to operate in the country.
The Iraqi interior ministry said the ban followed the firm's "improper conduct and excessive use of force" in the 2007 incident.