In 1683 he aided the Holy Roman Emperor at Vienna in the battle against the Turks. In 1691 he became governor of the Spanish Netherlands.
His first marriage, on 15 July 1685, was to Marie Antonie of Austria, daughter of Leopold I, Holy Roman Emperor.
His second marriage, on 12 January 1695, was to Therese Kunigunde, daughter of John III of Poland Sobieski.
Among their children were Charles VII Albert elector of Bavaria, who became Holy Roman Emperor. Their other son Klemens August of Bavaria, became imperial elector and archbishop of Cologne and of several other German dioceses. He was also the grandmaster of the Teutonic Knights.
During the Habsburg Spanish Inheritance wars Max Emanuel's family became separated and the sons were held prisoners for several years in Austria. There his son Klemens August was brought up by Jesuits. There were bloody scenes in Bavaria brought on by Austrian imperial troops. The people of Bavaria rose up. Only in 1715 was the family re-united.
The uncle Joseph Clemens, elector and archbishop of Cologne saw to it, that Klemens August of Bavaria received several appointments in Alt-Oetting, diocese Regensburg and at the Prince-Bishopric Berchtesgaden and he soon received papal confirmation as bishop of Regensburg, later Cologne.
Kurfuerst Maximilian Emanuel of Bavaria's fame is based above all on his conduct as general and his victories over the Turks.