In 1798, Alston was elected as a Federalist to the U.S. House, defeating incumbent Thomas Blount and two other candidates. Alston served from March 4, 1799, to March 4, 1815. Early in the Jefferson administration, Alston changed parties and became affiliated with the Republican Party. Local Federalists recruited former Gov. William R. Davie to challenge Alston in 1803, but Alston survived Davie's challenge. Alston chaired the House Committee on Revisal and Unfinished Business during the 13th U.S. Congress. In the election of April 1813, Alston defeated Daniel Mason, the Peace candidate, with the smallest margin of his re-election campaigns (56%-44%), and Alston retired at the end of the term.