After the war, Muhlenberg was elected to the Supreme Executive Council of the Commonwealth of Pennsylvania in 1784. He was elected Vice-President of the Council, a position comparable to that of Lieutenant Governor, on October 31, 1787. His term as Vice-President ended on a mysterious note. On October 14, 1788 the minutes of the Executive Council report that Muhlenberg had left Philadelphia without tendering his resignation—why his resignation was needed or expected is not noted—so a messenger was sent after him. That night, after the messenger returned with the resignation, the Council met at President Benjamin Franklin's home to choose Muhlenberg's successor, electing David Redick to the position.