Ford suffered from complications related to diabetes since childhood and also had renal dysfunction which required dialysis and, in 2000, a kidney transplant, which improved his quality of life considerably. He was found dead from natural causes in his Minneapolis home on September 25, 2006, by his partner since the mid-1990s, Elise Matthesen. He was a prominent member of the "Friends of the Minneapolis Public Library", which established a "John M. Ford Book Endowment" after his death with the donations to be used as interest-generating capital for yearly purchase of new books.