The Indian College educational experiment ended in 1670, when its building was devoted to printing. A few years later, King Philip's War, a movement led by the Wampanoag sachem Metacomet (King Philip), in protest against colonial expansion and Christianization, destroyed many communities, undermining cultural relations and eroding support for programs like the Indian College. In 1698, the Indian College’s empty and crumbling building was dismantled. Its bricks were used to build the original Stoughton Hall, itself torn down in 1781.
The ideal of Harvard's 1650 charter was revitalized three hundred years after the Indian College’s dissolution when Native students returned to Harvard, and in the 1970s, the Harvard University Native American Program (HUNAP) was created to train leaders and educators. In 1997, the Indian College commemorative plaque was unveiled to honor the first Native Americans to attend Harvard College. It was placed on Matthews Hall near the original location of the Indian College.