In 1718, Belcher was elected to the Massachusetts council and became colonial governor when his predecessor died. Initially accepted by Boston, his popularity decreased when he brought the censure of the English government. He was later appointed governor of the province of New Jersey and assisted in the founding of the College of New Jersey (now known as Princeton University), including building the library for the new school.
Belchertown, in western Massachusetts, is named for him. His son, also named Jonathan Belcher, was the Lt. Gov of Nova Scotia. He was the uncle of Lt. Gov Andrew Oliver and Chief Justice Peter Oliver, and was also the great-grandfather of Admiral Edward Belcher.