Muhlenberg was elected to the 1st Congress (1789–1791) as one of the at-large representatives from Pennsylvania. His brother Frederick was the Speaker of the House for that same Congress. He was the first founder of the Democratic-Republican Societies in 1793. Muhlenberg served in Congress as a Republican during the 3rd Congress 1793–1795 and 5th Congress 1799–1801 for the 1st district. Muhlenberg was elected by the legislature to the U.S. Senate on a second ballot in February 1801 over George Logan, but resigned on June 30 of that same year.