He then established a private legal practice in Concord, New Hampshire and became active in the Republican Party.

In 1859, Prescott became editor of the Independent Democrat, a Republican newspaper that opposed slavery and endorsed the Abraham Lincoln administration.

Prescott was a New England special agent for the United States Department of the Treasury from 1865 to 1869, responsible to audit and report on the activities of customs collectors at border crossing and ports.

In addition to his political activities, Prescott was an author and was involved with several historical organizations.

The Benjamin Franklin Prescott House is listed on the National Register of Historic Places.