TD Bank claims that the singer's Steve Stoute Foundation for the Advancement of Women Now took out a loan for over $250,000 in June 2011 and has yet to pay back the sum.
Blige set up the foundation in 2008, as well as the Mary J Blige Centre for Women in 2009.
According to court documents obtained by TMZ, Blige's foundation was to pay the loan back by December 2011. However, when the time came, the organisation made only a $368 (£235) payment.
Demands for payment in writing were made by the bank on February 7 and 29, with no response from the charity.
The foundation is the subject of another lawsuit launched by musicians from a 2011 gala who claim they were not paid for their work. The organisation also failed to file a federal tax return for 2010.
A rep for Blige said that the foundation is "presently transitioning its management and headquarters".
The representative added: "We remain committed to our mandate of helping women gain the confidence and skills necessary to reach their full individual potential."
Blige was involved in another controversy earlier this year when her advert for Burger King's crispy chicken wraps was pulled due to complaints of "buffoonery".