Muhlenberg was born to Pennsylvania German parents Anna and Henry Muhlenberg in Trappe, Pennsylvania. He was sent, together with his brothers, Frederick Augustus and Gotthilf Henry Ernst in 1763 to Halle. They were educated in Latin at the Francke Foundations. He left school in 1767 to start as a sales assistant in Lübeck and returned in the same year to Pennsylvania. There he received a classical education from the Academy of Philadelphia, which is today the University of Pennsylvania.