In 1788 Bowdoin served as a member of the Massachusetts convention that ratified the United States Constitution. A strong supporter of Federalism, Bowdoin worked hard for its ratification, bringing a skeptical Samuel Adams and his supporters into the fold by inviting him to a dinner with other pro-ratification delegates, and offering Federalist support to John Hancock in future elections. Bowdoin's Federalist supporters backed Hancock in the 1789 election, even though Bowdoin also stood for election. He remained active in his charitable and scientific pursuits in his later years, continuing his leadership of the American Academy of Arts and Sciences as well as that of the Humane Society. He also continued to engage in new business ventures, buying in 1789 an interest in one of the first American merchant ships to sail to China.