He died in Boston on November 6, 1790, of "putrid fever and dysentery". Bowdoin's funeral was one of the largest of the time in Boston, with people lining the streets to view the funeral procession. He was interred in Boston's Granary Burying Ground. Among his bequests was a gift to Harvard College for awards that are now known as the Bowdoin Prizes. His son James III donated lands from the family estate in Brunswick, Maine, as well as funds and books, to establish Bowdoin College in his honor.