The younger Benjamin graduated from Harvard College in 1766[3] and joined his father in the merchant business.

After adoption of the United States Constitution, Goodhue was elected to the First and to the three succeeding Congresses and served from March 4, 1789, until his resignation in June 1796.

[3] Goodhue was a supporter of the strong central government, and joined the Federalist Party when it was organized.

He served as chairman of the Committee on Commerce and Manufactures in the Fourth United States Congress.

He was elected in 1796 to the United States Senate, filling a vacancy caused by the resignation of George Cabot.