Born in Graz, little is known about his first years of life. His first notorious presence was in 1592, when Maximilian Ernest and his mother accompanied his older sister Anna to marry King Sigismund III of Poland.
Together with his brother Ferdinand and his cousins Maximilian III and Matthias, Maximilian Ernest signed a document dated 25 April 1606 in Vienna, under which his cousin, Emperor Rudolf II, was declared incapable of governing because of his mental illness and Matthias could assumed the Headship of the Habsburg territories as regent.
His cousin Maximilian III, called the German Grand Master (der Deutschmeister), allowed Maximiliam Ernest to join the Teutonic Knights in 1615, and one year later, in 1616, he appointed him Landkomtur of the Bailiwick of Austria. Already named Coadjutor of the Teutonic Order was determined that Maximilian Ernest would succeeded his cousin in the office of Grand Master, but he died unexpectedly aged thirty-two, unmarried and childless (however he left an illegitimate son, Don Carlos d'Austria, who died in 1638). He was buried in the Seckau Abbey.