He was born in Megeve, Savoy, (now in France), and of Scottish descent. He studied in Paris with Jean Baptiste Lully between 1663 and 1669, then became an organist in Molsheim and Sélestat. Later, he studied law in Ingolstadt, afterwards settling in Vienna. He could not get an official appointment, so he travelled to Prague in 1677, then to Salzburg, where he worked for the archbishop for some ten years.
About 1680, he traveled to Italy, there studying the organ with Bernardo Pasquini, a follower of the tradition of Girolamo Frescobaldi; he also met Arcangelo Corelli, whose works he admired very much. From 1690 to his death, he was Kapellmeister to the bishop of Passau.
Georg Muffat should not be confused with his son Gottlieb Muffat, also a successful composer.