He returned to court for long enough to marry Maria Antonia, daughter of Leopold I, Holy Roman Emperor and Margaret Theresa of Spain, on 15 July 1685 in Vienna, Austria.

[3][4][2] In the War of the Grand Alliance he again fought on the Habsburgs' side, protecting the Rhine frontier, and, being the Emperor's son-in-law and the husband of the King of Spain's niece, was appointed governor of the Spanish Netherlands in late 1691.

[7] However, he concentrated his interests in Western Europe, making his sons by Theresa Kunegunda Sobieska, Charles Albert and Clemens August, the principal beneficiaries of his ambitions.

In 1704–05, following the evacuation of the Bavarian court to the Spanish Netherlands after the defeat at the Battle of Blenheim, Max Emanuel's consort apparently was in charge of the government in the Stewardship of Munich of the Electorate of Bavaria as Regent Princess.

In the ensuing evacuation of his court to the Netherlands, Maximilian Emanuel's family became separated and his sons were held prisoners for several years in Austria, Clemens August being brought up by Jesuits.

[10] Maximilian Emanuel was again forced to flee the Netherlands after the Battle of Ramillies on 23 May 1706 and found refuge at the French court in Versailles where his late sister Maria Anna (1660–1690) had been the Dauphine of France.

It was bitter for him to witness the royal elevation of the German princes Augustus II the Strong (1697), Frederick I of Prussia (1701) and George I of Hanover (1714) as well as of his cousin Victor Amadeus of Sicily (1713) while his own political dreams could not be realized.

The Wittelsbach prince-electors Max Emanuel, his son Clemens August of Cologne, Charles III Philip, Elector Palatine and Franz Ludwig of Trier had at that time four votes at their disposal for the next imperial election.

With the appointment of Joseph Effner serving as chief architect of the court and the young François de Cuvilliés as his assistant, the French influence significantly increased and Max Emanuel's return in 1715 marked the origin of the era of Bavarian Rococo.